Plant caffeic acid 3-0-methyltransferase homologs

ABSTRACT

This invention relates to an isolated nucleic acid fragment encoding a protein involved in phenylpropanoid metabolism. The invention also relates to the construction of a chimeric gene encoding all or a portion of the protein involved in phenylpropanoid metabolism, in sense or antisense orientation, wherein expression of the chimeric gene results in production of altered levels of the protein involved in phenylpropanoid metabolism in a transformed host cell.

[0001] This application claims the benefit of U.S. Provisional Application No. 60/119,587, filed Feb. 10, 1999.

FIELD OF THE INVENTION

[0002] This invention is in the field of plant molecular biology. More specifically, this invention pertains to nucleic acid fragments encoding proteins involved in phenylpropanoid metabolism in plants and seeds.

BACKGROUND OF THE INVENTION

[0003] Plant cells and tissues can respond to mechanical, chemical or pathogen induced injury by producing various phenolic compounds including mono- or dimethoxylated lignin precursors derived from cinnamic acid via a complex series of biochemical reactions. These lignin precursors are eventually used by the plant to produce the lignin polymer which helps in wound repair by adding hydrophobicity, a physical barrier against pathogen infection and mechanical strength to the injured tissue (Vance, C. P., et al., 1980, Annu Rev Phytopathol 18:259-288). Biosynthesis of the mono- or dimethoxylated lignin precursors occures, in part, by the action of two enzymes, caffeic acid 3-O-methyltransferase (COMT), also known as caffeic acid/5-hydroxyferulic acid O-methyltransferase and caffeoyl CoA 3-O-methyltransferase (CCOMT). Both enzymes have been isolated and purified from a wide variety of plant species.

[0004] Studies have shown that the activities of COMT and CCOMT increase prior to lignin deposition (Inoue, K., et al., 1998, Plant Physiol 117(3):761-770). Synthesis of lignin precursors involves the methylation of caffeic acid to yeild ferulic acid followed by 5-hydroxylation of ferulate then a second methyltion to yield sinapate. COMT has been implicated in the methylation of both caffeic acid and 5-hydroxyferulic acid ((Inoue, K., et al., 1998, Plant Physiol 117(3):761-770). Research indicates that COMT transcripts are present at high levels in organs containing vascular tisssue and one study suggests that antisense inhibition of COMT can lead to modified lignin content and composition in the xylem and phloem of transgenic plant tissue (Dwivedi, U., et al., 1994, Plant Mol. Biol. 26:61-71).

[0005] Because of lignins importance in cell wall architecture and wound repair mechanisms there is considerable interest. in the prospects for altering lignin quantity or quality by genetic engineering. For example, chemical treatments needed to remove lignin during the paper-pulping process are expensive and environmentally unfriendly. Plants with altered lignin quantity or quality could benefit this industry (Boudet, A., et al., 1996, Mol Breeding 2:25-39; Campbell, M., et al., 1996, Plant Physiol 110:3-13). Thus, there is a great deal of interest in identifying the genes that encode proteins involved in the production of lignin in plants. These genes may be used in plant cells to control lignin production. Accordingly, the availability of nucleic acid sequences encoding all or a portion of an enzyme involved in the production of lignin would facilitate studies to better understand lignin production in plant cells and provide genetic tools to enhance or otherwise alter lignin biosynthesis which in turn could provide mechanisms to control cell wall architecture and host defence and injury repair mechanisms in plant cells.

SUMMARY OF THE INVENTION

[0006] The present invention relates to isolated polynucleotides comprising a nucleotide sequence encoding a polypeptide of at least 305 amino acids that has at least 92% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of a corn caffeic acid 3-O-methyltransferase polypeptide of SEQ ID NO: 8, rice caffeic acid 3-O-methyltransferase polypeptides of SEQ ID NOs: 2, 10 and 16, soybean caffeic acid 3-O-methyltransferase polypeptides of SEQ ID NOs: 4 and 12, and wheat caffeic acid 3-O-methyltransferase polypeptides of SEQ ID NOs: 6 and 14. The present invention also relates to an isolated polynucleotide comprising the complement of the nucleotide sequences described above.

[0007] The present invention relates to isolated polynucleotides comprising a nucleotide sequence encoding a polypeptide of at least 50 amino acids that has at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs: 18, 20, 22, 24 and 28. The present invention also relates to an isolated polynucleotide comprising the complement of the nucleotide sequences described above.

[0008] It is preferred that the isolated polynucleotides of the claimed invention consists of a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25 and 27 that codes for the polypeptide selected from the group consisting of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, and 28. The present invention also relates to an isolated polynucleotide comprising a nucleotide sequences of at least one of 60 (preferably at least one of 40, most preferably at least one of 30) contiguous nucleotides derived from a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27 and the complement of such nucleotide sequences.

[0009] The present invention relates to a chimeric gene comprising an isolated polynucleotide of the present invention operably linked to suitable regulatory sequences.

[0010] The present invention relates to an isolated host cell comprising a chimeric gene of the present invention or an isolated polynucleotide of the present invention. The host cell may be eukaryotic, such as a yeast or a plant cell, or prokaryotic, such as a bacterial cell. The present invention also relates to a virus, preferably a baculovirus, comprising an isolated polynucleotide of the present invention or a chimeric gene of the present invention.

[0011] The present invention relates to a process for producing an isolated host cell comprising a chimeric gene of the present invention or an isolated polynucleotide of the present invention, the process comprising either transforming or transfecting an isolated compatible host cell with a chimeric gene or isolated polynucleotide of the present invention.

[0012] The present invention relates to a caffeic acid 3-O-methyltransferase polypeptide of at least 305 amino acids comprising at least 92% homology based on the Clustal method of alignment compared to a polypeptide selected from the group consisting of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14 and 16.

[0013] The present invention relates to a method of selecting an isolated polynucleotide that affects the level of expression of a caffeic acid 3-O-methyltransferase polypeptide in a host cell, preferably a plant cell, the method comprising the steps of: (a) constructing an isolated polynucleotide of the present invention or an isolated chimeric gene of the present invention; (b) introducing the isolated polynucleotide or the isolated chimeric gene into a host cell; (c) measuring the level a caffeic acid 3-O-methyltransferase polypeptide in the host cell containing the isolated polynucleotide; and (d) comparing the level of a caffeic acid 3-O-methyltransferase polypeptide in the host cell containing the isolated polynucleotide with the level of a caffeic acid 3-O-methyltransferase polypeptide in the host cell that does not contain the isolated polynucleotide.

[0014] The present invention relates to a method of obtaining a nucleic acid fragment encoding a substantial portion of a caffeic acid 3-O-methyltransferase polypeptide gene, preferably a plant caffeic acid 3-O-methyltransferase polypeptide gene, comprising the steps of: synthesizing an oligonucleotide primer comprising a nucleotide sequence of at least one of 60 (preferably at least one of 40, most preferably at least one of 30) contiguous nucleotides derived from a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27 and the complement of such nucleotide sequences; and amplifying a nucleic acid fragment (preferably a cDNA inserted in a cloning vector) using the oligonucleotide primer. The amplified nucleic acid fragment preferably will encode a portion of a caffeic acid 3-O-methyltransferase amino acid sequence.

[0015] The present invention also relates to a method of obtaining a nucleic acid fragment encoding all or a substantial portion of the amino acid sequence encoding a caffeic acid 3-O-methyltransferase polypeptide comprising the steps of: probing a cDNA or genomic library with an isolated polynucleotide of the present invention; identifying a DNA clone that hybridizes with an isolated polynucleotide of the present invention; isolating the identified DNA clone; and sequencing the cDNA or genomic fragment that comprises the isolated DNA clone.

[0016] The present invention relates to a composition, such as a hybridization mixture, comprising an isolated polynucleotide of the present invention.

[0017] The present invention relates to an isolated polynucleotide of the present invention comprising at least one of 30 contiguous nucleotides derived from a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25 and 27.

[0018] The present invention relates to an expression cassette comprising an isolated polynucleotide of the present invention operably linked to a promoter.

[0019] The present invention relates to a method for positive selection of a transformed cell comprising: (a) transforming a host cell with the chimeric gene of the present invention or an expression cassette of the present invention; and (b) growing the transformed host cell, preferably plant cell, such as a monocot or a dicot, under conditions which allow expression of the caffeic acid 3-O-methyltransferase polynucleotide in an amount sufficient to complement a null mutant and alter methylation of both caffeic acid and 5-hydroxyferulic acid to provide a positive selection means.

BRIEF DESCRIPTION OF THE SEQUENCE DESCRIPTIONS

[0020] The invention can be more fully understood from the following detailed description and the accompanying Sequence Listing which form a part of this application.

[0021] Table 1 lists the polypeptides that are described herein, the designation of the cDNA clones that comprise the nucleic acid fragments encoding polypeptides representing all or a substantial portion of these polypeptides, and the corresponding identifier (SEQ ID NO:) as used in the attached Sequence Listing. Table 1 also identifies the cDNA clones as individual ESTs (“EST”), the sequences of the entire cDNA inserts comprising the indicated cDNA clones (“FIS”), contigs assembled from two or more ESTs (“Contig”), contigs assembled from an FIS and one or more ESTs (“Contig*”), or sequences encoding the entire protein derived from an FIS, a contig, or an FIS and PCR (“CGS”). Nucleotide sequences, SEQ ID NOs: 3, 5, 9, 11, 13 and 15 and amino acid sequences SEQ ID NOs: 4, 6, 10, 12, 14 and 16 were determined by further sequence analysis of cDNA clones encoding the amino acid sequences set forth in SEQ ID NOs: 4, 6, 10, 12, 14 and 16. Nucleotide SEQ ID NOs: 1, 17, 19, 21, 23, 25 and 27 and amino acid SEQ ID NOs: 2, 18, 20, 22, 24, 26 and 28 were presented in a U.S. Provisional Application No. 60/119,587, filed Feb. 10, 1999.

[0022] The sequence descriptions and Sequence Listing attached hereto comply with the rules governing nucleotide and/or amino acid sequence disclosures in patent applications as set forth in 37 C.F.R. §1.821-1.825. TABLE 1 Proteins Involved in Phenylpropanoid Metabolism SEQ ID NO: Protein Clone Designation (Nucleotide) (Amino Acid) Caffeic acid 3-0- Contig composed of:  1  2 methyltransferase rl0n.pk084.c19 rls48.pk0011.d2 rr1.pk0011.a10 rsl1n.pk001.c5 Caffeic acid 3-O- se2.27d08 CGS  3  4 methyltransferase Caffeic acid 3-O- wlm96.pk033.c5 CGS  5  6 methyltransferase Caffeic acid 3-O- Contig composed of:  7  8 methyltransferase cpg1c.pk016.m11 cr1n.pk0031.e3 p0092.chwaj20r Caffeic acid 3-O- rlr24.pk0094.b11 CGS  9 10 methyltransferase Caffeic acid 3-O- srr3c.pk002.h5 CGS 11 12 methyltransferase Caffeic acid 3-O- wlm96.pk025.c3 CGS 13 14 methyltransferase Caffeic acid 3-O- rlr6.pk0035.a3 CGS 15 16 methyltransferase Caffeic acid 3-O- Contig composed of: 17 18 methyltransferase se2.27d08 se4.12b11 srr1c.pk002.o15 ss1.pk0036.g7 Caffeic acid 3-O- Contig composed of: 19 20 methyltransferase wdk9n.pk001.h14 wlk4.pk0009.2 wlm96.pk033.c5 Caffeic acid 3-O- Contig composed of: 21 22 methyltransferase rlr24.pk0094.b11 rr1.pk083.n7 rsr9n.pk005.d1 Caffeic acid 3-O- srr3c.pk002.h5 EST 23 24 methyltransferase Caffeic acid 3-O- Contig composed of: 25 26 methyltransferase wlm96.pk025.c3 wlm96.pk034.p19 wlm96.pk038.f14 Caffeic acid 3-O- Contig composed of: 27 28 methyltransferase rl0n.pk0018.e3 rl0n.pk0071.f10 rlr6.pk0035.a3 rls48.pk0008.f12 rsr9n.pk003.i18

[0023] The Sequence Listing contains the one letter code for nucleotide sequence characters and the three letter codes for amino acids as defined in conformity with the IUPAC-IUBMB standards described in Nucleic Acids Res. 13:3021-3030 (1985) and in the Biochemical J. 219 (No. 2):345-373 (1984) which are herein incorporated by reference. The symbols and format used for nucleotide and amino acid sequence data comply with the rules set forth in 37 C.F.R. §1.822.

DETAILED DESCRIPTION OF THE INVENTION

[0024] In the context of this disclosure, a number of terms shall be utilized. As used herein, a “polynucleotide” is a nucleotide sequence such as a nucleic acid fragment. A polynucleotide may be a polymer of RNA or DNA that is single- or double-stranded, that optionally contains synthetic, non-natural or altered nucleotide bases. A polynucleotide in the form of a polymer of DNA may be comprised of one or more segments of cDNA, genomic DNA, synthetic DNA, or mixtures thereof. An isolated polynucleotide of the present invention may include at least one of 60 contiguous nucleotides, preferably at least one of 40 contiguous nucleotides, most preferably one of at least 30 contiguous nucleotides derived from SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27 or the complement of such sequences.

[0025] As used herein, “contig” refers to a nucleotide sequence that is assembled from two or more constituent nucleotide sequences that share common or overlapping regions of sequence homology. For example, the nucleotide sequences of two or more nucleic acid fragments can be compared and aligned in order to identify common or overlapping sequences. Where common or overlapping sequences exist between two or more nucleic acid fragments, the sequences (and thus their corresponding nucleic acid fragments) can be assembled into a single contiguous nucleotide sequence.

[0026] As used herein, “substantially similar” refers to nucleic acid fragments wherein changes in one or more nucleotide bases results in substitution of one or more amino acids, but do not affect the functional properties of the polypeptide encoded by the nucleotide sequence. “Substantially similar” also refers to nucleic acid fragments wherein changes in one or more nucleotide bases does not affect the ability of the nucleic acid fragment to mediate alteration of gene expression by gene silencing through for example antisense or co-suppression technology. “Substantially similar” also refers to modifications of the nucleic acid fragments of the instant invention such as deletion or insertion of one or more nucleotides that do not substantially affect the functional properties of the resulting transcript vis-à-vis the ability to mediate gene silencing or alteration of the functional properties of the resulting protein molecule. It is therefore understood that the invention encompasses more than the specific exemplary nucleotide or amino acid sequences and includes functional equivalents thereof.

[0027] Substantially similar nucleic acid fragments may be selected by screening nucleic acid fragments representing subfragments or modifications of the nucleic acid fragments of the instant invention, wherein one or more nucleotides are substituted, deleted and/or inserted, for their ability to affect the level of the polypeptide encoded by the unmodified nucleic acid fragment in a plant or plant cell. For example, a substantially similar nucleic acid fragment representing at least one of 30 contiguous nucleotides derived from the instant nucleic acid fragment can be constructed and introduced into a plant or plant cell. The level of the polypeptide encoded by the unmodified nucleic acid fragment present in a plant or plant cell exposed to the substantially similar nucleic fragment can then be compared to the level of the polypeptide in a plant or plant cell that is not exposed to the substantially similar nucleic acid fragment.

[0028] For example, it is well known in the art that antisense suppression and co-suppression of gene expression may be accomplished using nucleic acid fragments representing less than the entire coding region of a gene, and by nucleic acid fragments that do not share 100% sequence identity with the gene to be suppressed. Moreover, alterations in a nucleic acid fragment which result in the production of a chemically equivalent amino acid at a given site, but do not effect the functional properties of the encoded polypeptide, are well known in the art. Thus, a codon for the amino acid alanine, a hydrophobic amino acid, may be substituted by a codon encoding another less hydrophobic residue, such as glycine, or a more hydrophobic residue, such as valine, leucine, or isoleucine. Similarly, changes which result in substitution of one negatively charged residue for another, such as aspartic acid for glutamic acid, or one positively charged residue for another, such as lysine for arginine, can also be expected to produce a functionally equivalent product. Nucleotide changes which result in alteration of the N-terminal and C-terminal portions of the polypeptide molecule would also not be expected to alter the activity of the polypeptide. Each of the proposed modifications is well within the routine skill in the art, as is determination of retention of biological activity of the encoded products. Consequently, an isolated polynucleotide comprising a nucleotide sequence of at least one of 60 (preferably at least one of 40, most preferably at least one of 30) contiguous nucleotides derived from a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27 and the complement of such nucleotide sequences may be used in methods of selecting an isolated polynucleotide that affects the expression of a polypeptide (caffeic acid 3-O-methyltransferase) in a host cell. A method of selecting an isolated polynucleotide that affects the level of expression of a polypeptide in a host cell (eukaryotic, such as plant or yeast, prokaryotic such as bacterial, or viral) may comprise the steps of: constructing an isolated polynucleotide of the present invention or an isolated chimeric gene of the present invention; introducing the isolated polynucleotide or the isolated chimeric gene into a host cell; measuring the level a polypeptide in the host cell containing the isolated polynucleotide; and comparing the level of a polypeptide in the host cell containing the isolated polynucleotide with the level of a polypeptide in a host cell that does not contain the isolated polynucleotide.

[0029] Moreover, substantially similar nucleic acid fragments may also be characterized by their ability to hybridize. Estimates of such homology are provided by either DNA-DNA or DNA-RNA hybridization under conditions of stringency as is well understood by those skilled in the art (Hames and Higgins, Eds. (1985) Nucleic Acid Hybridisation, IRL Press, Oxford, U.K.). Stringency conditions can be adjusted to screen for moderately similar fragments, such as homologous sequences from distantly related organisms, to highly similar fragments, such as genes that duplicate functional enzymes from closely related organisms. Post-hybridization washes determine stringency conditions. One set of preferred conditions uses a series of washes starting with 6×SSC, 0.5% SDS at room temperature for 15 min, then repeated with 2×SSC, 0.5% SDS at 45° C. for 30 min, and then repeated twice with 0.2×SSC, 0.5% SDS at 50° C. for 30 min. A more preferred set of stringent conditions uses higher temperatures in which the washes are identical to those above except for the temperature of the final two 30 min washes in 0.2×SSC, 0.5% SDS was increased to 6.0° C. Another preferred set of highly stringent conditions uses two final washes in 0.1×SSC, 0.1% SDS at 65° C.

[0030] Substantially similar nucleic acid fragments of the instant invention may also be characterized by the percent identity of the amino acid sequences that they encode to the amino acid sequences disclosed herein, as determined by algorithms commonly employed by those skilled in this art. Suitable nucleic acid fragments (isolated polynucleotides of the present invention) encode polypeptides that are at least about 70% identical, preferably at least about 80% identical to the amino acid sequences reported herein. Preferred nucleic acid fragments encode amino acid sequences that are about 85% identical to the amino acid sequences reported herein. More preferred nucleic acid fragments encode amino acid sequences that are at least about 90% identical to the amino acid sequences reported herein. Most preferred are nucleic acid fragments that encode amino acid sequences that are at least about 95% identical to the amino acid sequences reported herein. Suitable nucleic acid fragments not only have the above homologies but typically encode a polypeptide having at least 50 amino acids, preferably at least 100 amino acids, more preferably at least 150 amino acids, still more preferably at least 200 amino acids, and most preferably at least 250 amino acids. Sequence alignments and percent identity calculations were performed using the Megalign program of the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wis.). Multiple alignment of the sequences was performed using the Clustal method of alignment (Higgins and Sharp (1989) CABIOS. 5:151-153) with the default parameters (GAP PENALTY=10, GAP LENGTH PENALTY=10). Default parameters for pairwise alignments using the Clustal method were KTUPLE 1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5.

[0031] A “substantial portion” of an amino acid or nucleotide sequence comprises an amino acid or a nucleotide sequence that is sufficient to afford putative identification of the protein or gene that the amino acid or nucleotide sequence comprises. Amino acid and nucleotide sequences can be evaluated either manually by one skilled in the art, or by using computer-based sequence comparison and identification tools that employ algorithms such as BLAST (Basic Local Alignment Search Tool; Altschul et al. (1993) J. Mol. Biol. 215:403-410; see also www.ncbi.nlm.nih.gov/BLAST/). In general, a sequence of ten or more contiguous amino acids or thirty or more contiguous nucleotides is necessary in order to putatively identify a polypeptide or nucleic acid sequence as homologous to a known protein or gene. Moreover, with respect to nucleotide sequences, gene-specific oligonucleotide probes comprising 30 or more contiguous nucleotides may be used in sequence-dependent methods of gene identification (e.g., Southern hybridization) and isolation (e.g. in situ hybridization of bacterial colonies or bacteriophage plaques). In addition, short oligonucleotides of 12 or more nucleotides may be used as amplification primers in PCR in order to obtain a particular nucleic acid fragment comprising the primers. Accordingly, a “substantial portion” of a nucleotide sequence comprises a nucleotide sequence that will afford specific identification and/or isolation of a nucleic acid fragment comprising the sequence. The instant specification teaches amino acid and nucleotide sequences encoding polypeptides that comprise one or more particular plant proteins. The skilled artisan, having the benefit of the sequences as reported herein, may now use all or a substantial portion of the disclosed sequences for purposes known to those skilled in this art. Accordingly, the instant invention comprises the complete sequences as reported in the accompanying Sequence Listing, as well as substantial portions of those sequences as defined above.

[0032] “Codon degeneracy” refers to divergence in the genetic code permitting variation of the nucleotide sequence without effecting the amino acid sequence of an encoded polypeptide. Accordingly, the instant invention relates to any nucleic acid fragment comprising a nucleotide sequence that encodes all or a substantial portion of the amino acid sequences set forth herein. The skilled artisan is well aware of the “codon-bias” exhibited by a specific host cell in usage of nucleotide codons to specify a given amino acid. Therefore, when synthesizing a nucleic acid fragment for improved expression in a host cell, it is desirable to design the nucleic acid fragment such that its frequency of codon usage approaches the frequency of preferred codon usage of the host cell.

[0033] “Synthetic nucleic acid fragments” can be assembled from oligonucleotide building blocks that are chemically synthesized using procedures known to those skilled in the art. These building blocks are ligated and annealed to form larger nucleic acid fragments which may then be enzymatically assembled to construct the entire desired nucleic acid fragment. “Chemically synthesized”, as related to nucleic acid fragment, means that the component nucleotides were assembled in vitro. Manual chemical synthesis of nucleic acid fragments may be accomplished using well established procedures, or automated chemical synthesis can be performed using one of a number of commercially available machines. Accordingly, the nucleic acid fragments can be tailored for optimal gene expression based on optimization of nucleotide sequence to reflect the codon bias of the host cell. The skilled artisan appreciates the likelihood of successful gene expression if codon usage is biased towards those codons favored by the host. Determination of preferred codons can be based on a survey of genes derived from the host cell where sequence information is available.

[0034] “Gene” refers to a nucleic acid fragment that expresses a specific protein, including regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence. “Native gene” refers to a gene as found in nature with its own regulatory sequences. “Chimeric gene” refers any gene that is not a native gene, comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. “Endogenous gene” refers to a native gene in its natural location in the genome of an organism. A “foreign” gene refers to a gene not normally found in the host organism, but that is introduced into the host organism by gene transfer. Foreign genes can comprise native genes inserted into a non-native organism, or chimeric genes. A “transgene” is a gene that has been introduced into the genome by a transformation procedure.

[0035] “Coding sequence” refers to a nucleotide sequence that codes for a specific amino acid sequence. “Regulatory sequences” refer to nucleotide sequences located upstream (5′ non-coding sequences), within, or downstream (3′ non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, translation leader sequences, introns, and polyadenylation recognition sequences.

[0036] “Promoter” refers to a nucleotide sequence capable of controlling the expression of a coding sequence or functional RNA. In general, a coding sequence is located 3′ to a promoter sequence. The promoter sequence consists of proximal and more distal upstream elements, the latter elements often referred to as enhancers. Accordingly, an “enhancer” is a nucleotide sequence which can stimulate promoter activity and may be an innate element of the promoter or a heterologous element inserted to enhance the level or tissue-specificity of a promoter. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic nucleotide segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental conditions. Promoters which cause a nucleic acid fragment to be expressed in most cell types at most times are commonly referred to as “constitutive promoters”. New promoters of various types useful in plant cells are constantly being discovered; numerous examples may be found in the compilation by Okamuro and Goldberg (1989) Biochemistry of Plants 15:1-82. It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, nucleic acid fragments of different lengths may have identical promoter activity.

[0037] The “translation leader sequence” refers to a nucleotide sequence located between the promoter sequence of a gene and the coding sequence. The translation leader sequence is present in the fully processed mRNA upstream of the translation start sequence. The translation leader sequence may affect processing of the primary transcript to mRNA, mRNA stability or translation efficiency. Examples of translation leader sequences have been described (Turner and Foster (1995) Mol. Biotechnol. 3:225-236).

[0038] The “3′ non-coding sequences” refer to nucleotide sequences located downstream of a coding sequence and include polyadenylation recognition sequences and other sequences encoding regulatory signals capable of affecting mRNA processing or gene expression. The polyadenylation signal is usually characterized by affecting the addition of polyadenylic acid tracts to the 3′ end of the mRNA precursor. The use of different 3′ non-coding sequences is exemplified by Ingelbrecht et al. (1989) Plant Cell 1:671-680.

[0039] “RNA transcript” refers to the product resulting from RNA polymerase-catalyzed transcription of a DNA sequence. When the RNA transcript is a perfect complementary copy of the DNA sequence, it is referred to as the primary transcript or it may be a RNA sequence derived from posttranscriptional processing of the primary transcript and is referred to as the mature RNA. “Messenger RNA (mRNA)” refers to the RNA that is without introns and that can be translated into polypeptide by the cell. “cDNA” refers to a double-stranded DNA that is complementary to and derived from mRNA. “Sense” RNA refers to an RNA transcript that includes the mRNA and so can be translated into a polypeptide by the cell. “Antisense RNA” refers to an RNA transcript that is complementary to all or part of a target primary transcript or mRNA and that blocks the expression of a target gene (see U.S. Pat. No. 5,107,065, incorporated herein by reference). The complementarity of an antisense RNA may be with any part of the specific nucleotide sequence, i.e., at the 5′ non-coding sequence, 3′ non-coding sequence, introns, or the coding sequence. “Functional RNA” refers to sense RNA, antisense RNA, ribozyme RNA, or other RNA that may not be translated but yet has an effect on cellular processes.

[0040] The term “operably linked” refers to the association of two or more nucleic acid fragments on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in sense or antisense orientation.

[0041] The term “expression”, as used herein, refers to the transcription and stable accumulation of sense (mRNA) or antisense RNA derived from the nucleic acid fragment of the invention. Expression may also refer to translation of mRNA into a polypeptide. “Antisense inhibition” refers to the production of antisense RNA transcripts capable of suppressing the expression of the target protein. “Overexpression” refers to the production of a gene product in transgenic organisms that exceeds levels of production in normal or non-transformed organisms. “Co-suppression” refers to the production of sense RNA transcripts capable of suppressing the expression of identical or substantially similar foreign or endogenous genes (U.S. Pat. No. 5,231,020, incorporated herein by reference).

[0042] “Altered levels” refers to the production of gene product(s) in transgenic organisms in amounts or proportions that differ from that of normal or non-transformed organisms.

[0043] “Mature” protein refers to a post-translationally processed polypeptide; i.e., one from which any pre- or propeptides present in the primary translation product have been removed. “Precursor” protein refers to the primary product of translation of mRNA; i.e., with pre- and propeptides still present. Pre- and propeptides may be but are not limited to intracellular localization signals.

[0044] A “chloroplast transit peptide” is an amino acid sequence which is translated in conjunction with a protein and directs the protein to the chloroplast or other plastid types present in the cell in which the protein is made. “Chloroplast transit sequence” refers to a nucleotide sequence that encodes a chloroplast transit peptide. A “signal peptide” is an amino acid sequence which is translated in conjunction with a protein and directs the protein to the secretory system (Chrispeels (1991) Ann. Rev. Plant Phys. Plant Mol. Biol. 42:21-53). If the protein is to be directed to a vacuole, a vacuolar targeting signal (supra) can further be added, or if to the endoplasmic reticulum, an endoplasmic reticulum retention signal (supra) may be added. If the protein is to be directed to the nucleus, any signal peptide present should be removed and instead a nuclear localization signal included (Raikhel (1992) Plant Phys. 100:1627-1632).

[0045] “Transformation” refers to the transfer of a nucleic acid fragment into the genome of a host organism, resulting in genetically stable inheritance. Host organisms containing the transformed nucleic acid fragments are referred to as “transgenic” organisms. Examples of methods of plant transformation include Agrobacterium-mediated transformation (De Blaere et al. (1987) Meth. Enzymol. 143:277) and particle-accelerated or “gene gun” transformation technology (Klein et al. (1987) Nature (London) 327:70-73; U.S. Pat. No. 4,945,050, incorporated herein by reference).

[0046] Standard recombinant DNA and molecular cloning techniques used herein are well known in the art and are described more fully in Sambrook et al. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, 1989 (hereinafter “Maniatis”).

[0047] Nucleic acid fragments encoding at least a portion of several proteins involved in phenylpropanoid metabolism have been isolated and identified by comparison of random plant cDNA sequences to public databases containing nucleotide and protein sequences using the BLAST algorithms well known to those skilled in the art. The nucleic acid fragments of the instant invention may be used to isolate cDNAs and genes encoding homologous proteins from the same or other plant species. Isolation of homologous genes using sequence-dependent protocols is well known in the art. Examples of sequence-dependent protocols include, but are not limited to, methods of nucleic acid hybridization, and methods of DNA and RNA amplification as exemplified by various uses of nucleic acid amplification technologies (e.g., polymerase chain reaction, ligase chain reaction).

[0048] For example, genes encoding other caffeic acid 3-O-methyltransferase proteins, either as cDNAs or genomic DNAs, could be isolated directly by using all or a portion of the instant nucleic acid fragments as DNA hybridization probes to screen libraries from any desired plant employing methodology well known to those skilled in the art. Specific oligonucleotide probes based upon the instant nucleic acid sequences can be designed and synthesized by methods known in the art (Maniatis). Moreover, the entire sequences can be used directly to synthesize DNA probes by methods known to the skilled artisan such as random primer DNA labeling, nick translation, or end-labeling techniques, or RNA probes using available in vitro transcription systems. In addition, specific primers can be designed and used to amplify a part or all of the instant sequences. The resulting amplification products can be labeled directly during amplification reactions or labeled after amplification reactions, and used as probes to isolate full length cDNA or genomic fragments under conditions of appropriate stringency.

[0049] In addition, two short segments of the instant nucleic acid fragments may be used in polymerase chain reaction protocols to amplify longer nucleic acid fragments encoding homologous genes from DNA or RNA. The polymerase chain reaction may also be performed on a library of cloned nucleic acid fragments wherein the sequence of one primer is derived from the instant nucleic acid fragments, and the sequence of the other primer takes advantage of the presence of the polyadenylic acid tracts to the 3′ end of the mRNA precursor encoding plant genes. Alternatively, the second primer sequence may be based upon sequences derived from the cloning vector. For example, the skilled artisan can follow the RACE protocol (Frohman et al. (1988) Proc. Natl. Acad. Sci. USA 85:8998-9002) to generate cDNAs by using PCR to amplify copies of the region between a single point in the transcript and the 3′ or 5′ end. Primers oriented in the 3′ and 5′ directions can be designed from the instant sequences. Using commercially available 3′ RACE or 5′ RACE systems (BRL), specific 3′ or 5′ cDNA fragments can be isolated (Ohara et al. (1989) Proc. Natl. Acad. Sci. USA 86:5673-5677; Loh et al. (1989) Science 243:217-220). Products generated by the 3′ and 5′ RACE procedures can be combined to generate full-length cDNAs (Frohman and Martin (1989) Techniques 1:165). Consequently, a polynucleotide comprising a nucleotide sequence of at least one of 60 (preferably one of at least 40, most preferably one of at least 30) contiguous nucleotides derived from a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27 and the complement of such nucleotide sequences may be used in such methods to obtain a nucleic acid fragment encoding a substantial portion of an amino acid sequence of a polypeptide. The present invention relates to a method of obtaining a nucleic acid fragment encoding a substantial portion of a polypeptide of a gene (such as caffeic acid 3-O-methyltransferase) preferably a substantial portion of a plant polypeptide of a gene, comprising the steps of: synthesizing an oligonucleotide primer comprising a nucleotide sequence of at least one of 60 (preferably at least one of 40, most preferably at least one of 30) contiguous nucleotides derived from a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27 and the complement of such nucleotide sequences; and amplifying a nucleic acid fragment (preferably a cDNA inserted in a cloning vector) using the oligonucleotide primer. The amplified nucleic acid fragment preferably will encode a portion of a polypeptide (caffeic acid 3-O-methyltransferase).

[0050] Availability of the instant nucleotide and deduced amino acid sequences facilitates immunological screening of cDNA expression libraries. Synthetic peptides representing portions of the instant amino acid sequences may be synthesized. These peptides can be used to immunize animals to produce polyclonal or monoclonal antibodies with specificity for peptides or proteins comprising the amino acid sequences. These antibodies can be then be used to screen cDNA expression libraries to isolate full-length cDNA clones of interest (Lerner (1984) Adv. Immunol. 36:1-34; Maniatis).

[0051] The nucleic acid fragments of the instant invention may be used to create transgenic plants in which the disclosed polypeptides are present at higher or lower levels than normal or in cell types or developmental stages in which they are not normally found. This would have the effect of altering the level of methylation of both caffeic acid and 5-hydroxyferulic acid in those cells.

[0052] Overexpression of the proteins of the instant invention may be accomplished by first constructing a chimeric gene in which the coding region is operably linked to a promoter capable of directing expression of a gene in the desired tissues at the desired stage of development. The chimeric gene may comprise promoter sequences and translation leader sequences derived from the same genes. 3′ Non-coding sequences encoding transcription termination signals may also be provided. The instant chimeric gene may also comprise one or more introns in order to facilitate gene expression.

[0053] Plasmid vectors comprising the isolated polynucleotide (or chimeric gene) may be constructed. The choice of plasmid vector is dependent upon the method that will be used to transform host plants. The skilled artisan is well aware of the genetic elements that must be present on the plasmid vector in order to successfully transform, select and propagate host cells containing the chimeric gene. The skilled artisan will also recognize that different independent transformation events will result in different levels and patterns of expression (Jones et al. (1985) EMBO J. 4:2411-2418; De Almeida et al. (1989) Mol. Gen. Genetics 218:78-86), and thus that multiple events must be screened in order to obtain lines displaying the desired expression level and pattern. Such screening may be accomplished by Southern analysis of DNA, Northern analysis of mRNA expression, Western analysis of protein expression, or phenotypic analysis.

[0054] For some applications it may be useful to direct the instant polypeptides to different cellular compartments, or to facilitate its secretion from the cell. It is thus envisioned that the chimeric gene described above may be further supplemented by directing the coding sequence to encode the instant polypeptides with appropriate intracellular targeting sequences such as transit sequences (Keegstra (1989) Cell 56:247-253), signal sequences or sequences encoding endoplasmic reticulum localization (Chrispeels (1991) Ann. Rev. Plant Phys. Plant Mol. Biol. 42:21-53), or nuclear localization signals (Raikhel (1992) Plant Phys. 100: 1627-1632) with or without removing targeting sequences that are already present. While the references cited give examples of each of these, the list is not exhaustive and more targeting signals of use may be discovered in the future.

[0055] It may also be desirable to reduce or eliminate expression of genes encoding the instant polypeptides in plants for some applications. In order to accomplish this, a chimeric gene designed for co-suppression of the instant polypeptide can be constructed by linking a gene or gene fragment encoding that polypeptide to plant promoter sequences. Alternatively, a chimeric gene designed to express antisense RENA for all or part of the instant nucleic acid fragment can be constructed by linking the gene or gene fragment in reverse orientation to plant promoter sequences. Either the co-suppression or antisense chimeric genes could be introduced into plants via transformation wherein expression of the corresponding endogenous genes are reduced or eliminated.

[0056] Molecular genetic solutions to the generation of plants with altered gene expression have a decided advantage over more traditional plant breeding approaches. Changes in plant phenotypes can be produced by specifically inhibiting expression of one or more genes by antisense inhibition or cosuppression (U.S. Pat. Nos. 5,190,931, 5,107,065 and 5,283,323). An antisense or cosuppression construct would act as a dominant negative regulator of gene activity. While conventional mutations can yield negative regulation of gene activity these effects are most likely recessive. The dominant negative regulation available with a transgenic approach may be advantageous from a breeding perspective. In addition, the ability to restrict the expression of specific phenotype to the reproductive tissues of the plant by the use of tissue specific promoters may confer agronomic advantages relative to conventional mutations which may have an effect in all tissues in which a mutant gene is ordinarily expressed.

[0057] The person skilled in the art will know that special considerations are associated with the use of antisense or cosuppression technologies in order to reduce expression of particular genes. For example, the proper level of expression of sense or antisense genes may require the use of different chimeric genes utilizing different regulatory elements known to the skilled artisan. Once transgenic plants are obtained by one of the methods described above, it will be necessary to screen individual transgenics for those that most effectively display the desired phenotype. Accordingly, the skilled artisan will develop methods for screening large numbers of transformants. The nature of these screens will generally be chosen on practical grounds. For example, one can screen by looking for changes in gene expression by using antibodies specific for the protein encoded by the gene being suppressed, or one could establish assays that specifically measure enzyme activity. A preferred method will be one which allows large numbers of samples to be processed rapidly, since it will be expected that a large number of transformants will be negative for the desired phenotype.

[0058] The instant polypeptides (or portions thereof) may be produced in heterologous host cells, particularly in the cells of microbial hosts, and can be used to prepare antibodies to the these proteins by methods well known to those skilled in the art. The antibodies are useful for detecting the polypeptides of the instant invention in situ in cells or in vitro in cell extracts. Preferred heterologous host cells for production of the instant polypeptides are microbial hosts. Microbial expression systems and expression vectors containing regulatory sequences that direct high level expression of foreign proteins are well known to those skilled in the art. Any of these could be used to construct a chimeric gene for production of the instant polypeptides. This chimeric gene could then be introduced into appropriate microorganisms via transformation to provide high level expression of the encoded phenylpropanoid metabolism protein. An example of a vector for high level expression of the instant polypeptides in a bacterial host is provided (Example 6).

[0059] All or a substantial portion of the nucleic acid fragments of the instant invention may also be used as probes for genetically and physically mapping the genes that they are a part of, and as markers for traits linked to those genes. Such information may be useful in plant breeding in order to develop lines with desired phenotypes. For example, the instant nucleic acid fragments may be used as restriction fragment length polymorphism (RFLP) markers. Southern blots (Maniatis) of restriction-digested plant genomic DNA may be probed with the nucleic acid fragments of the instant invention. The resulting banding patterns may then be subjected to genetic analyses using computer programs such as MapMaker (Lander et al. (1987) Genomics 1:174-181) in order to construct a genetic map. In addition, the nucleic acid fragments of the instant invention may be used to probe Southern blots containing restriction endonuclease-treated genomic DNAs of a set of individuals representing parent and progeny of a defined genetic cross. Segregation of the DNA polymorphisms is noted and used to calculate the position of the instant nucleic acid sequence in the genetic map previously obtained using this population (Botstein et al. (1980) Am. J. Hum. Genet. 32:314-331).

[0060] The production and use of plant gene-derived probes for use in genetic mapping is described in Bernatzky and Tanksley (1986) Plant Mol. Biol. Reporter 4:37-41. Numerous publications describe genetic mapping of specific cDNA clones using the methodology outlined above or variations thereof. For example, F2 intercross populations, backcross populations, randomly mated populations, near isogenic lines, and other sets of individuals may be used for mapping. Such methodologies are well known to those skilled in the art.

[0061] Nucleic acid probes derived from the instant nucleic acid sequences may also be used for physical mapping (i.e., placement of sequences on physical maps; see Hoheisel et al. In: Nonmammalian Genomic Analysis: A Practical Guide, Academic press 1996, pp. 319-346, and references cited therein).

[0062] In another embodiment, nucleic acid probes derived from the instant nucleic acid sequences may be used in direct fluorescence in situ hybridization (FISH) mapping (Trask (1991) Trends Genet. 7:149-154). Although current methods of FISH mapping favor use of large clones (several to several hundred KB; see Laan et al. (1995) Genome Res. 5:13-20), improvements in sensitivity may allow performance of FISH mapping using shorter probes.

[0063] A variety of nucleic acid amplification-based methods of genetic and physical mapping may be carried out using the instant nucleic acid sequences. Examples include allele-specific amplification (Kazazian (1989) J. Lab. Clin. Med. 11:95-96), polymorphism of PCR-amplified fragments (CAPS; Sheffield et al. (1993) Genomics 16:325-332), allele-specific ligation (Landegren et al. (1988) Science 241:1077-1080), nucleotide extension reactions (Sokolov (1990) Nucleic Acid Res. 18:3671), Radiation Hybrid Mapping (Walter et al. (1997) Nat. Genet. 7:22-28) and Happy Mapping (Dear and Cook (1989) Nucleic Acid Res. 17:6795-6807). For these methods, the sequence of a nucleic acid fragment is used to design and produce primer pairs for use in the amplification reaction or in primer extension reactions. The design of such primers is well known to those skilled in the art. In methods employing PCR-based genetic mapping, it may be necessary to identify DNA sequence differences between the parents of the mapping cross in the region corresponding to the instant nucleic acid sequence. This, however, is generally not necessary for mapping methods.

[0064] Loss of function mutant phenotypes may be identified for the instant cDNA clones either by targeted gene disruption protocols or by identifying specific mutants for these genes contained in a maize population carrying mutations in all possible genes (Ballinger and Benzer (1989) Proc. Natl. Acad. Sci USA 86:9402-9406; Koes et al. (1995) Proc. Natl. Acad Sci USA 92:8149-8153; Bensen et al. (1995) Plant Cell 7:75-84). The latter approach may be accomplished in two ways. First, short segments of the instant nucleic acid fragments may be used in polymerase chain reaction protocols in conjunction with a mutation tag sequence primer on DNAs prepared from a population of plants in which Mutator transposons or some other mutation-causing DNA element has been introduced (see Bensen, supra). The amplification of a specific DNA fragment with these primers indicates the insertion of the mutation tag element in or near the plant gene encoding the instant polypeptides. Alternatively, the instant nucleic acid fragment may be used as a hybridization probe against PCR amplification products generated from the mutation population using the mutation tag sequence primer in conjunction with an arbitrary genomic site primer, such as that for a restriction enzyme site-anchored synthetic adaptor. With either method, a plant containing a mutation in the endogenous gene encoding the instant polypeptides can be identified and obtained. This mutant plant can then be used to determine or confirm the natural function of the instant polypeptides disclosed herein.

EXAMPLES

[0065] The present invention is further defined in the following Examples, in which all parts and percentages are by weight and degrees are Celsius, unless otherwise stated. It should be understood that these Examples, while indicating preferred embodiments of the invention, are given by way of illustration only. From the above discussion and these Examples, one skilled in the art can ascertain the essential characteristics of this invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the invention to adapt it to various usages and conditions.

Example 1

[0066] Composition of cDNA Libraries; Isolation and Sequencing of cDNA Clones

[0067] cDNA libraries representing mRNAs from various corn, rice, soybean and wheat tissues were prepared. The characteristics of the libraries are described below. TABLE 2 cDNA Libraries from Corn, Rice, Soybean and Wheat Library Tissue Clone cpg1c Corn pooled BMS treated with chemicals cpg1c.pk0016.m11 related to RNA, DNA synthesis** cr1n Corn Root From 7 Day Old Seedlings* cr1n.pk0031.e3 p0092 Corn Husks* p0092.chwaj20r rl0n Rice 15 Day Old Leaf* rl0n.pk0018.e3 rl0n.pk084.c19 rl0n.pk0071.f10 rlr6 Rice Leaf 15 Days After Germination, rlr6.pk0035.a3 6 Hours After Infection of Strain Magaporthe grisea 4360-R-62 (AVR2-YAMO); Resistant rlr24 Rice Leaf 15 Days After Germination, rlr24.pk0094.b11 24 Hours After Infection of Strain Magaporthe grisea 4360-R-62 (AVR2-YAMO); Resistant rls48 Rice Leaf 15 Days After Germination, rls48.pk0008.f12 48 Hours After Infection of Strain rls48.pk011.d2 Magaporthe grisea 4360-R-67 (AVR2-YAMO); Susceptible rr1 Rice Root of Two Week Old Developing rr1.pk0011.a10 Seedling rr1.pk083.n7 rsr9n Rice Leaf 15 Days After Germination rsr9n.pk003.i18 Harvested 2-72 Hours Following Infection rsr9n.pk005.d1 With Magnaporta grisea (4360-R-62 and 4360-R-67)* rsl1n Rice 15-Day-Old Seedling* rsl1n.pk001.c5 se2 Soybean Embryo, 13 Days After se2.27d08 Flowering se4 Soybean Embryo, 19 Days After se4.12b11 Flowering srr3c Soybean 8-Day-Old Root srr3c.pk002.h5 srr1c Soybean 8-Day-Old Root srr1c.pk002.o15 ss1 Soybean Seedling 5-10 Days After ss1.pk0036.g7 Germination wlk4 Wheat Seedlings 4 Hours After Treatment wlk4.pk0009.e2 With fungicide*** wdk9n Wheat Kernels 3, 7, 14 and 21 Days After wdk9n.pk001.h14 Anthesis wlm96 Wheat Seedlings 96 Hours After wlm96.pk025.c3 Inoculation With Erysiphe graminis wlm96.pk034.p19 f. sp tritici wlm96.pk033.c5 wlm96.pk038.f14

[0068] cDNA libraries may be prepared by any one of many methods available. For example, the cDNAs may be introduced into plasmid vectors by first preparing the cDNA libraries in Uni-ZAP™ XR vectors according to the manufacturer's protocol (Stratagene Cloning Systems, La Jolla, Calif.). The Uni-ZAP™ XR libraries are converted into plasmid libraries according to the protocol provided by Stratagene. Upon conversion, cDNA inserts will be contained in the plasmid vector pBluescript. In addition, the cDNAs may be introduced directly into precut Bluescript II SK(+) vectors (Stratagene) using T4 DNA ligase (New England Biolabs), followed by transfection into DH10B cells according to the manufacturer's protocol (GIBCO BRL Products). Once the cDNA inserts are in plasmid vectors, plasmid DNAs are prepared from randomly picked bacterial colonies containing recombinant pBluescript plasmids, or the insert cDNA sequences are amplified via polymerase chain reaction using primers specific for vector sequences flanking the inserted cDNA sequences. Amplified insert DNAs or plasmid DNAs are sequenced in dye-primer sequencing reactions to generate partial cDNA sequences (expressed sequence tags or “ESTs”; see Adams et al., (1991) Science 252:1651-1656). The resulting ESTs are analyzed using a Perkin Elmer Model 377 fluorescent sequencer.

Example 2

[0069] Identification of cDNA Clones

[0070] cDNA clones encoding caffeic acid 3-O-methyltransferase proteins were identified by conducting BLAST (Basic Local Alignment Search Tool; Altschul et al. (1993) J. Mol. Biol. 215:403-410; see also www.ncbi.nlm.nih.gov/BLAST/) searches for similarity to sequences contained in the BLAST “nr” database (comprising all non-redundant GenBank CDS translations, sequences derived from the 3-dimensional structure Brookhaven Protein Data Bank, the last major release of the SWISS-PROT protein sequence database, EMBL, and DDBJ databases). The cDNA sequences obtained in Example 1 were analyzed for similarity to all publicly available DNA sequences contained in the “nr” database using the BLASTN algorithm provided by the National Center for Biotechnology Information (NCBI). The DNA sequences were translated in all reading frames and compared for similarity to all publicly available protein sequences contained in the “nr” database using the BLASTX algorithm (Gish and States (1993) Nat. Genet. 3:266-272) provided by the NCBI. For convenience, the P-value (probability) of observing a match of a cDNA sequence to a sequence contained in the searched databases merely by chance as calculated by BLAST are reported herein as “pLog” values, which represent the negative of the logarithm of the reported P-value. Accordingly, the greater the pLog value, the greater the likelihood that the cDNA sequence and the BLAST “hit” represent homologous proteins.

Example 3

[0071] Characterization of cDNA Clones Encoding Caffeic Acid 3-O-methyltransferase

[0072] The BLASTX search using the EST sequences from clones listed in Table 3 revealed similarity of the polypeptides encoded by the cDNAs to caffeic acid 3-O-methyltransferase from Zea mays (NCBI Identifier No. gi 729135), Medicago sativa (NCBI Identifier No. gi 116908), Stylosanthes humilis (NCBI Identifier No. gi 1582580), Lolium perenne (NCBI Identifier No. gi 2388664), Lolium perenne (NCBI Identifier No. gi 4104220), Arabidopsis thaliana (NCBI Identifier No. gi 6630734), Hordeum vulgare (NCBI Identifier No. gi 1314742), Populus kitakamiensis (NCBI Identifier No. gi 762870) and Populus kitakamiensis (NCBI Identifier No. gi 542050). Shown in Table 3 are the BLAST results for individual ESTs (“EST”), the sequences of the entire cDNA inserts comprising the indicated cDNA clones (“FIS”), contigs assembled from two or more ESTs (“Contig”), contigs assembled from an FIS and one or more ESTs (“Contig*”), or sequences encoding the entire protein derived from an FIS, a contig, or an FIS and PCR (“CGS”): TABLE 3 BLAST Results for Sequences Encoding Polypeptides Homologous to Zea mays, Medicago sativa, Stylosanthes humilis, Lolium perenne, Arabidopsis thaliana, Hordeum vulgare, Populus kitakamiensis and Populus kitakamiensis Caffeic Acid 3-O-methyltransferase Clone Status BLAST pLog Score Contig composed of: Contig 134.00 (gi 729135) rl0n.pk084.c19 rls48.pk0011.d2 rr1.pk0011.a10 rsl1n.pk001.c5 se2.27d08 CGS >254.00 (gi 152580) wlm96.pk033.c5 CGS >254.00 (gi 4104220) Contig composed of: Contig 72.52 (gi 6630734) cpg1c.pk016.m11 cr1n.pk0031.e3 p0092.chwaj20r rlr24.pk0094.b11 CGS 103.00 (gi 1314742) srr3c.pk002.h5 CGS 115.00 (gi 542050) wlm96.pk025.c3 CGS 147.00 (gi 4104220) rlr6.pk0035.a3 CGS 101.00 (gi 1314742)

[0073] TABLE 4 Percent Identity of Amino Acid Sequences Deduced From the Nucleotide Sequences of cDNA Clones Encoding Polypeptides Homologous to Zea mays, Medicago sativa, Stylosanthes humilis, Lolium perenne, Arabidopsis thaliana, Hordeum vulgare, Populus kitakamiensis and Populus kitakamiensis Caffeic Acid 3-O-methyltransferase SEQ ID NO. Percent Identity to  2 74% (gi 729135)   4 90% (gi 1582580)  6 89% (gi 4104220)  8 62% (gi 6630734) 10 48% (gi 1314742) 12 52% (gi 542050)  14 69% (gi 4104220) 16 47% (gi 1314742)

[0074] The data in Table 4 represents a calculation of the percent identity of the amino acid sequences set forth in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14 and 16 and the Zea mays, Medicago sativa, Stylosanthes humilis, Lolium perenne, Arabidopsis thaliana, Hordeum vulgare, Populus kitakamiensis and Populus kitakamiensis sequences. The percent identity between the SEQ ID NOs ranged from 25% to 90%.

[0075] Sequence alignments and percent identity calculations were performed using the Megalign program of the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wis.). Multiple alignment of the sequences was performed using the Clustal method of alignment (Higgins and Sharp (1989) CABIOS. 5:151-153) with the default parameters (GAP PENALTY=10, GAP LENGTH PENALTY=10). Default parameters for pairwise alignments using the Clustal method were KTUPLE 1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5. Sequence alignments and BLAST scores and probabilities indicate that the nucleic acid fragments comprising the instant cDNA clones encode a substantial portion of a caffeic acid 3-O-methyltransferase. These sequences represent the first corn, rice, soybean and wheat sequences encoding caffeic acid 3-O-methyltransferase.

Example 4

[0076] Expression of Chimeric Genes in Monocot Cells

[0077] A chimeric gene comprising a cDNA encoding the instant polypeptides in sense orientation with respect to the maize 27 kD zein promoter that is located 5′ to the cDNA fragment, and the 10 kD zein 3′ end that is located 3′ to the cDNA fragment, can be constructed. The cDNA fragment of this gene may be generated by polymerase chain reaction (PCR) of the cDNA clone using appropriate oligonucleotide primers. Cloning sites (NcoI or SmaI) can be incorporated into the oligonucleotides to provide proper orientation of the DNA fragment when inserted into the digested vector pML 103 as described below. Amplification is then performed in a standard PCR. The amplified DNA is then digested with restriction enzymes NcoI and SmaI and fractionated on an agarose gel. The appropriate band can be isolated from the gel and combined with a 4.9 kb NcoI-SmaI fragment of the plasmid pML 103. Plasmid pML 103 has been deposited under the terms of the Budapest Treaty at ATCC (American Type Culture Collection, 10801 University Blvd., Manassas, Va. 20110-2209), and bears accession number ATCC 97366. The DNA segment from pML 103 contains a 1.05 kb SalI-NcoI promoter fragment of the maize 27 kD zein gene and a 0.96 kb SmaI-SalI fragment from the 3′ end of the maize 10 kD zein gene in the vector pGem9Zf(+) (Promega). Vector and insert DNA can be ligated at 15° C. overnight, essentially as described (Maniatis). The ligated DNA may then be used to transform E. coli XL1-Blue (Epicurian Coli XL-1 Blue™; Stratagene). Bacterial transformants can be screened by restriction enzyme digestion of plasmid DNA and limited nucleotide sequence analysis using the dideoxy chain termination method (Sequenase™ DNA Sequencing Kit; U.S. Biochemical). The resulting plasmid construct would comprise a chimeric gene encoding, in the 5′ to 3′ direction, the maize 27 kD zein promoter, a cDNA fragment encoding the instant polypeptides, and the 10 kD zein 3′ region.

[0078] The chimeric gene described above can then be introduced into corn cells by the following procedure. Immature corn embryos can be dissected from developing caryopses derived from crosses of the inbred corn lines H99 and LH132. The embryos are isolated 10 to 11 days after pollination when they are 1.0 to 1.5 mm long. The embryos are then placed with the axis-side facing down and in contact with agarose-solidified N6 medium (Chu et al. (1975) Sci. Sin. Peking 18:659-668). The embryos are kept in the dark at 27° C. Friable embryogenic callus consisting of undifferentiated masses of cells with somatic proembryoids and embryoids borne on suspensor structures proliferates from the scutellum of these immature embryos. The embryogenic callus isolated from the primary explant can be cultured on N6 medium and sub-cultured on this medium every 2 to 3 weeks.

[0079] The plasmid, p35S/Ac (obtained from Dr. Peter Eckes, Hoechst Ag, Frankfurt, Germany) may be used in transformation experiments in order to provide for a selectable marker. This plasmid contains the Pat gene (see European Patent Publication 0 242 236) which encodes phosphinothricin acetyl transferase (PAT). The enzyme PAT confers resistance to herbicidal glutamine synthetase inhibitors such as phosphinothricin. The pat gene in p35S/Ac is under the control of the 35S promoter from Cauliflower Mosaic Virus (Odell et al. (1985) Nature 313:810-812) and the 3′ region of the nopaline synthase gene from the T-DNA of the Ti plasmid of Agrobacterium tumefaciens.

[0080] The particle bombardment method (Klein et al. (1987) Nature 327:70-73) may be used to transfer genes to the callus culture cells. According to this method, gold particles (1 μm in diameter) are coated with DNA using the following technique. Ten μg of plasmid DNAs are added to 50 μL of a suspension of gold particles (60 mg per mL). Calcium chloride (50 μL of a 2.5 M solution) and spermidine free base (20 μL of a 1.0 M solution) are added to the particles. The suspension is vortexed during the addition of these solutions. After 10 minutes, the tubes are briefly centrifuged (5 sec at 15,000 rpm) and the supernatant removed. The particles are resuspended in 200 μL of absolute ethanol, centrifuged again and the supernatant removed. The ethanol rinse is performed again and the particles resuspended in a final volume of 30 μL of ethanol. An aliquot (5 μL) of the DNA-coated gold particles can be placed in the center of a Kapton™ flying disc (Bio-Rad Labs). The particles are then accelerated into the corn tissue with a Biolistic™ PDS-1000/He (Bio-Rad Instruments, Hercules Calif.), using a helium pressure of 1000 psi, a gap distance of 0.5 cm and a flying distance of 1.0 cm.

[0081] For bombardment, the embryogenic tissue is placed on filter paper over agarose-solidified N6 medium. The tissue is arranged as a thin lawn and covered a circular area of about 5 cm in diameter. The petri dish containing the tissue can be placed in the chamber of the PDS-1000/He approximately 8 cm from the stopping screen. The air in the chamber is then evacuated to a vacuum of 28 inches of Hg. The macrocarrier is accelerated with a helium shock wave using a rupture membrane that bursts when the He pressure in the shock tube reaches 1000 psi.

[0082] Seven days after bombardment the tissue can be transferred to N6 medium that contains gluphosinate (2 mg per liter) and lacks casein or proline. The tissue continues to grow slowly on this medium. After an additional 2 weeks the tissue can be transferred to fresh N6 medium containing gluphosinate. After 6 weeks, areas of about 1 cm in diameter of actively growing callus can be identified on some of the plates containing the glufosinate-supplemented medium. These calli may continue to grow when sub-cultured on the selective medium.

[0083] Plants can be regenerated from the transgenic callus by first transferring clusters of tissue to N6 medium supplemented with 0.2 mg per liter of 2,4-D. After two weeks the tissue can be transferred to regeneration medium (Fromm et al. (1990) Biotechnology 8:833-839).

Example 5

[0084] Expression of Chimeric Genes in Dicot Cells

[0085] A seed-specific expression cassette composed of the promoter and transcription terminator from the gene encoding the β subunit of the seed storage protein phaseolin from the bean Phaseolus vulgaris (Doyle et al. (1986) J. Biol. Chem. 261:9228-9238) can be used for expression of the instant polypeptides in transformed soybean. The phaseolin cassette includes about 500 nucleotides upstream (5′) from the translation initiation codon and about 1650 nucleotides downstream (3′) from the translation stop codon of phaseolin. Between the 5′ and 3′ regions are the unique restriction endonuclease sites Nco I (which includes the ATG translation initiation codon), Sma I, Kpn I and Xba I. The entire cassette is flanked by Hind III sites.

[0086] The cDNA fragment of this gene may be generated by polymerase chain reaction (PCR) of the cDNA clone using appropriate oligonucleotide primers. Cloning sites can be incorporated into the oligonucleotides to provide proper orientation of the DNA fragment when inserted into the expression vector. Amplification is then performed as described above, and the isolated fragment is inserted into a pUC 18 vector carrying the seed expression cassette.

[0087] Soybean embryos may then be transformed with the expression vector comprising sequences encoding the instant polypeptides. To induce somatic embryos, cotyledons, 3-5 mm in length dissected from surface sterilized, immature seeds of the soybean cultivar A2872, can be cultured in the light or dark at 26° C. on an appropriate agar medium for 6-10 weeks. Somatic embryos which produce secondary embryos are then excised and placed into a suitable liquid medium. After repeated selection for clusters of somatic embryos which multiplied as early, globular staged embryos, the suspensions are maintained as described below.

[0088] Soybean embryogenic suspension cultures can maintained in 35 mL liquid media on a rotary shaker, 150 rpm, at 26° C. with florescent lights on a 16:8 hour day/night schedule. Cultures are subcultured every two weeks by inoculating approximately 35 mg of tissue into 35 mL of liquid medium.

[0089] Soybean embryogenic suspension cultures may then be transformed by the method of particle gun bombardment (Klein et al. (1987) Nature (London) 327:70-73, U.S. Pat. No. 4,945,050). A DuPont Biolistic™ PDS 1000/HE instrument (helium retrofit) can be used for these transformations.

[0090] A selectable marker gene which can be used to facilitate soybean transformation is a chimeric gene composed of the 35S promoter from Cauliflower Mosaic Virus (Odell et al. (1985) Nature 313:810-812), the hygromycin phosphotransferase gene from plasmid pJR225 (from E. coli; Gritz et al.(1983) Gene 25:179-188) and the 3′ region of the nopaline synthase gene from the T-DNA of the Ti plasmid of Agrobacterium tumefaciens. The seed expression cassette comprising the phaseolin 5′ region, the fragment encoding the instant polypeptides and the phaseolin 3′ region can be isolated as a restriction fragment. This fragment can then be inserted into a unique restriction site of the vector carrying the marker gene.

[0091] To 50 μL of a 60 mg/mL 1 μm gold particle suspension is added (in order): 5 μL DNA (1 μg/μL), 20 μl spermidine (0.1 M), and 50 μL CaCl₂ (2.5 M). The particle preparation is then agitated for three minutes, spun in a microfuge for 10 seconds and the supernatant removed. The DNA-coated particles are then washed once in 400 μL 70% ethanol and resuspended in 40 μL of anhydrous ethanol. The DNA/particle suspension can be sonicated three times for one second each. Five μL of the DNA-coated gold particles are then loaded on each macro carrier disk.

[0092] Approximately 300-400 mg of a two-week-old suspension culture is placed in an empty 60×15 mm petri dish and the residual liquid removed from the tissue with a pipette. For each transformation experiment, approximately 5-10 plates of tissue are normally bombarded. Membrane rupture pressure is set at 1100 psi and the chamber is evacuated to a vacuum of 28 inches mercury. The tissue is placed approximately 3.5 inches away from the retaining screen and bombarded three times. Following bombardment, the tissue can be divided in half and placed back into liquid and cultured as described above.

[0093] Five to seven days post bombardment, the liquid media may be exchanged with fresh media, and eleven to twelve days post bombardment with fresh media containing 50 mg/mL hygromycin. This selective media can be refreshed weekly. Seven to eight weeks post bombardment, green, transformed tissue may be observed growing from untransformed, necrotic embryogenic clusters. Isolated green tissue is removed and inoculated into individual flasks to generate new, clonally propagated, transformed embryogenic suspension cultures. Each new line may be treated as an independent transformation event. These suspensions can then be subcultured and maintained as clusters of immature embryos or regenerated into whole plants by maturation and germination of individual somatic embryos.

Example 6

[0094] Expression of Chimeric Genes in Microbial Cells

[0095] The cDNAs encoding the instant polypeptides can be inserted into the T7 E. coli expression vector pBT430. This vector is a derivative of pET-3a (Rosenberg et al. (1987) Gene 56:125-135) which employs the bacteriophage T7 RNA polymerase/T7 promoter, system. Plasmid pBT430 was constructed by first destroying the EcoR I and Hind III sites in pET-3a at their original positions. An oligonucleotide adaptor containing EcoR I and Hind III sites was inserted at the BamH I site of pET-3a. This created pET-3aM with additional unique cloning sites for insertion of genes into, the expression vector. Then, the Nde I site at the position of translation initiation was converted to an Nco I site using oligonucleotide-directed mutagenesis. The DNA sequence of pET-3aM in this region, 5′-CATATGG, was converted to 5′-CCCATGG in pBT430.

[0096] Plasmid DNA containing a cDNA may be appropriately digested to release a nucleic acid fragment encoding the protein. This fragment may then be purified on a 1% NuSieve GTG™ low melting agarose gel (FMC). Buffer and agarose contain 10 μg/ml ethidium bromide for visualization of the DNA fragment. The fragment can then be purified from the agarose gel by digestion with GELase™ (Epicentre Technologies) according to the manufacturer's instructions, ethanol precipitated, dried and resuspended in 20 μL of water. Appropriate oligonucleotide adapters may be ligated to the fragment using T4 DNA ligase (New England Biolabs, Beverly, Mass.) The fragment containing the ligated adapters can be purified from the excess adapters using low melting agarose as described above. The vector pBT430 is digested, dephosphorylated with alkaline phosphatase (NEB) and deproteinized with phenol/chloroform as described above. The prepared vector pBT430 and fragment can then be ligated at 16° C. for 15 hours followed by transformation into DH5 electrocompetent cells (GIBCO BRL). Transformants can be selected on agar plates containing LB media and 100 μg/mL ampicillin. Transformants containing the gene encoding the instant polypeptides are then screened for the correct orientation with respect to the T7 promoter by restriction enzyme analysis.

[0097] For high level expression, a plasmid clone with the cDNA insert in the correct orientation relative to the T7 promoter can be transformed into E. coli strain BL21(DE3) (Studier et al. (1986) J. Mol. Biol. 189:113-130). Cultures are grown in LB medium containing ampicillin (100 mg/L) at 25° C. At an optical density at 600 nm of approximately 1, IPTG (isopropylthio-β-galactoside, the inducer) can be added to a final concentration of 0.4 mM and incubation can be continued for 3 h at 25°. Cells are then harvested by centrifugation and re-suspended in 50 μL of 50 mM Tris-HCl at pH 8.0 containing 0.1 mM DTT and 0.2 mM phenyl methylsulfonyl fluoride. A small amount of 1 mm glass beads can be added and the mixture sonicated 3 times for about 5 seconds each time with a microprobe sonicator. The mixture is centrifuged and the protein concentration of the supernatant determined. One μg of protein from the soluble fraction of the culture can be separated by SDS-polyacrylamide gel electrophoresis. Gels can be observed for protein bands migrating at the expected molecular weight.

[0098] Various modifications of the invention in addition to those shown and described herein will be apparent to those skilled in the art from the foregoing description. Such modifications are also intended to fall within the scope of the appended claims.

[0099] The disclosure of each reference set forth above is incorporated herein by reference in its entirety.

1 28 1 1008 DNA Oryza sativa unsure (522) n = A, C, G or T 1 tgtatccagc ctcctcctcc ttcttctcca tcgccggcga gagagagaga gagttagcta 60 gctaggatgg gttctacagc cgccgacatg gccgcggcgg ccgacgagga ggcgtgcatg 120 tacgcgctgc agctggcgtc gtcgtcgatc ctgccgatga cgctcaagaa cgccatcgag 180 ctgggcctgc tcgagacgct gcagtccgcc gccgtcgccg gaggaggggg aaaggcggcg 240 ctgctgacgc cggcggaggt ggccgacaag ctgccgtcca aggcgaaccc ggcggcggcc 300 gacatggtgg accgcatgct ccgcctgctc gcctcctaca acgtcgtcag gtgcgagatg 360 gaggagggcg ccgacggcaa gctctcccgc cgctacgccg ccgcgccggt gtgcaagtgg 420 ctgacgccca acgaggacgg cgtctccatg gccgccctcg ccctcatgaa ccaggacaag 480 gtcctcatgg agagctggta ctaccttaag gacgcagctg gnaacggcgg catcccgttc 540 aacaaggcgt acgggatgac ggcgttcgag taccacggca cggacgcccg cttcaaccgc 600 gtcttcaacg agggcatgaa gaaccactcc gtcatcatca ccaagaagct gctcgacctc 660 tacaccggct tcgacgccgc ctccaccgtc gtcgacgtcg gcggcggcgt gggcgccact 720 gtggccgccg tcgtctcccg ccacccgcac atccggggga tcaactacga cctcccccac 780 gtcatctccg aggcgccgcc gtttccccgg ggtggagcac gtcggcggcg acatgttcgc 840 ctccgtgccc cgcggcggcg aacgcaatcc tgatgaagtg gatcctccaa cgactggagc 900 gaacgagcac tgcgcgcggc tgctcaagaa ctgctacgaa cgcgctgccg gagcacggga 960 aggtggtggt ggtggagtgc gtgtgccgga gagcttccaa cgcgaagg 1008 2 305 PRT Oryza sativa UNSURE (277) Xaa = ANY AMINO ACID 2 Met Gly Ser Thr Ala Ala Asp Met Ala Ala Ala Ala Asp Glu Glu Ala 1 5 10 15 Cys Met Tyr Ala Leu Gln Leu Ala Ser Ser Ser Ile Leu Pro Met Thr 20 25 30 Leu Lys Asn Ala Ile Glu Leu Gly Leu Leu Glu Thr Leu Gln Ser Ala 35 40 45 Ala Val Ala Gly Gly Gly Gly Lys Ala Ala Leu Leu Thr Pro Ala Glu 50 55 60 Val Ala Asp Lys Leu Pro Ser Lys Ala Asn Pro Ala Ala Ala Asp Met 65 70 75 80 Val Asp Arg Met Leu Arg Leu Leu Ala Ser Tyr Asn Val Val Arg Cys 85 90 95 Glu Met Glu Glu Gly Ala Asp Gly Lys Leu Ser Arg Arg Tyr Ala Ala 100 105 110 Ala Pro Val Cys Lys Trp Leu Thr Pro Asn Glu Asp Gly Val Ser Met 115 120 125 Ala Ala Leu Ala Leu Met Asn Gln Asp Lys Val Leu Met Glu Ser Trp 130 135 140 Tyr Tyr Leu Lys Asp Ala Ala Gly Asn Gly Gly Ile Pro Phe Asn Lys 145 150 155 160 Ala Tyr Gly Met Thr Ala Phe Glu Tyr His Gly Thr Asp Ala Arg Phe 165 170 175 Asn Arg Val Phe Asn Glu Gly Met Lys Asn His Ser Val Ile Ile Thr 180 185 190 Lys Lys Leu Leu Asp Leu Tyr Thr Gly Phe Asp Ala Ala Ser Thr Val 195 200 205 Val Asp Val Gly Gly Gly Val Gly Ala Thr Val Ala Ala Val Val Ser 210 215 220 Arg His Pro His Ile Arg Gly Ile Asn Tyr Asp Leu Pro His Val Ile 225 230 235 240 Ser Glu Ala Pro Pro Phe Pro Gly Val Glu His Val Gly Gly Asp Met 245 250 255 Phe Ala Ser Val Pro Arg Gly Ala Asn Ala Ile Leu Met Lys Trp Ile 260 265 270 Leu Gln Arg Leu Xaa Pro Asn Glu His Cys Ala Arg Leu Leu Lys Asn 275 280 285 Cys Tyr Asp Ala Leu Pro Glu His Gly Lys Val Val Val Val Glu Cys 290 295 300 Val 305 3 1370 DNA Glycine max 3 gcacgagcac aagctcacag agcaagaaca ctgttccaat acggaatcta aggcaaagca 60 aaccaaacat cttgaatcat gggttcaaca ggtgagactc agattacccc aacccacgta 120 tctgatgaag aagcaaacct tttcgccatg caactagcca gtgcttctgt ccttccaatg 180 atcctcaaat cagcacttga gcttgatctg ttggaaatca tagccaaggc tggccctggt 240 gttcatcttt cccccactga catttcttct cagctcccaa cacagaaccc tgatgcaccc 300 gttatgttgg accgtatatt gcgcctattg gcttgctaca atatcctctc tttttctctc 360 cgcactctcc ctgatggcaa ggttgagagg ctctatggtc tcgcccccgt tgccaagtac 420 ttggttaaga acgaagatgg tgtctccatt gctgcgctca acctcatgaa ccaggacaaa 480 gtcctcatgg aaagctggta ctatttgaaa gatgcagtcc ttgaaggagg cattccattt 540 aacaaggctt atggaatgac agcctttgag taccatggaa cagatccaag gtttaacaag 600 gttttcaaca agggaatggc tgatcactct accatcacaa tgaagaaaat tcttgagacc 660 tacacaggtt ttgagagtct taaatctctg gttgatgttg gtggtgggac tggagctgta 720 atcaacatga ttgtctcaaa gcatcccact attaagggca ttaattttga tttgcctcat 780 gtcattgaag atgccccatc ttatcctgga gtggagcatg taggtggaga tatgtttgcg 840 agtgttccga aagctgatgc tatttttatg aagtggattt gccacgattg gagtgatgag 900 cactgcttga agtttttgaa gaactgctac gaggcactac cagacaatgg gaaggtgatt 960 gtggcagaat gcattcttcc agtggctcca gactctagct tggccacaaa aggtgtggtt 1020 cacatcgatg tgatcatgtt ggcacataat ccacgtggga aagagagaac agagaaagag 1080 tttgaggctc tggccaaagg gtctggattc caaggtttcc gagttgtttg ctgtgctttc 1140 aataccaaca tcatggaatt tctcaaaaag atttaagttc tttggcatgg attcatgtca 1200 agctgcattt gggttttgag attgaggttg tggttgtggt gctactttcc aaagctttcc 1260 cggaaaaacg taattttctc ttaggaaaag aataatgaac aagttcaatg tagactgcca 1320 atatcaaata acaagtttca ttttgtggat taaaaaaaaa aaaaaaaaaa 1370 4 365 PRT Glycine max 4 Met Gly Ser Thr Gly Glu Thr Gln Ile Thr Pro Thr His Val Ser Asp 1 5 10 15 Glu Glu Ala Asn Leu Phe Ala Met Gln Leu Ala Ser Ala Ser Val Leu 20 25 30 Pro Met Ile Leu Lys Ser Ala Leu Glu Leu Asp Leu Leu Glu Ile Ile 35 40 45 Ala Lys Ala Gly Pro Gly Val His Leu Ser Pro Thr Asp Ile Ser Ser 50 55 60 Gln Leu Pro Thr Gln Asn Pro Asp Ala Pro Val Met Leu Asp Arg Ile 65 70 75 80 Leu Arg Leu Leu Ala Cys Tyr Asn Ile Leu Ser Phe Ser Leu Arg Thr 85 90 95 Leu Pro Asp Gly Lys Val Glu Arg Leu Tyr Gly Leu Ala Pro Val Ala 100 105 110 Lys Tyr Leu Val Lys Asn Glu Asp Gly Val Ser Ile Ala Ala Leu Asn 115 120 125 Leu Met Asn Gln Asp Lys Val Leu Met Glu Ser Trp Tyr Tyr Leu Lys 130 135 140 Asp Ala Val Leu Glu Gly Gly Ile Pro Phe Asn Lys Ala Tyr Gly Met 145 150 155 160 Thr Ala Phe Glu Tyr His Gly Thr Asp Pro Arg Phe Asn Lys Val Phe 165 170 175 Asn Lys Gly Met Ala Asp His Ser Thr Ile Thr Met Lys Lys Ile Leu 180 185 190 Glu Thr Tyr Thr Gly Phe Glu Ser Leu Lys Ser Leu Val Asp Val Gly 195 200 205 Gly Gly Thr Gly Ala Val Ile Asn Met Ile Val Ser Lys His Pro Thr 210 215 220 Ile Lys Gly Ile Asn Phe Asp Leu Pro His Val Ile Glu Asp Ala Pro 225 230 235 240 Ser Tyr Pro Gly Val Glu His Val Gly Gly Asp Met Phe Ala Ser Val 245 250 255 Pro Lys Ala Asp Ala Ile Phe Met Lys Trp Ile Cys His Asp Trp Ser 260 265 270 Asp Glu His Cys Leu Lys Phe Leu Lys Asn Cys Tyr Glu Ala Leu Pro 275 280 285 Asp Asn Gly Lys Val Ile Val Ala Glu Cys Ile Leu Pro Val Ala Pro 290 295 300 Asp Ser Ser Leu Ala Thr Lys Gly Val Val His Ile Asp Val Ile Met 305 310 315 320 Leu Ala His Asn Pro Arg Gly Lys Glu Arg Thr Glu Lys Glu Phe Glu 325 330 335 Ala Leu Ala Lys Gly Ser Gly Phe Gln Gly Phe Arg Val Val Cys Cys 340 345 350 Ala Phe Asn Thr Asn Ile Met Glu Phe Leu Lys Lys Ile 355 360 365 5 1314 DNA Triticum aestivum 5 caaacatggg ctccaccgca gccgacatgg ccgcctccgc cgacgaggag gcgtgcatgt 60 atgctctcca gctcgtctcg tcgtcgatcc tcccgatgac gctcaagaac gccatcgagc 120 tgggtctcct ggagaccctg gtggccgccg gcggcaagct gctgacgccc gccgaggtgg 180 cagccaagct cccgtccacg gcgaatcccg ccgcggcgga catggtggac cgcatgctcc 240 ggctgctggc ctcgtacaac gtggtgtcgt gcacgatgga ggagggcaag gacggccggc 300 tgtcccggcg gtacggcgcc gcgcccgtgt gcaagttcct cacccccaac gaagacggcg 360 tctccatggc ggcgctcgcg ctcatgaacc aggacaaggt cctcatggag agctggtact 420 acctgaagga cgcggtcctt gacggcggca tcccgttcaa caaggcgtac gggatgtcgg 480 cgttcgagta ccacggcacg gacccgcgct tcaaccgcgt cttcaacgag gggatgaaga 540 accactccat catcatcacc aagaagctcc tcgaggtcta caagggcttc gagggcctcg 600 gcaccatcgt cgacgtgggc ggcggcgtgg gcgccatcgt cgccgcctac ccggccatca 660 agggcatcaa cttcgacctc ccccacgtca tctccgaggc gccaccgttc ccgggcgtca 720 cccacgtcgg cggcgacatg ttccagaagg tgccctcggg cgacgccatc ctcatgaagt 780 ggatcctcca cgactggagc gacgagcact gcgcgacgct gctcaagaac tgctacgacg 840 cgctgccggc gcacggcaag gtggtgctcg tggagtgcat cctgccggtg aacccggagg 900 ccacgcccaa ggcgcagggg gtattccacg tcgacatgat catgctcgcg cacaaccccg 960 gcggcaggga gaggtacgag agggagttcg aggccctggc caagggcgcc ggcttcaaag 1020 ccatcaagac cacctacatc tacgccaacg catttgccat cgagttcacc aagtagatcc 1080 atgccaaccg tccaccgctc gctttgagac catcttcttc ttcctcgctg gcgctgctga 1140 atatgtactt tggcttgctg tttcctctgt tttcctaatt ttgtcatcct agctctgaat 1200 cattctgaat gctactggtt gtgccgtcga tctacccatt cgaaatgtac tgtactatta 1260 atagtgctgc tcttaaaggt tgcatgtgat gcaatgaaaa aaaaaaaaaa aaaa 1314 6 356 PRT Triticum aestivum 6 Met Gly Ser Thr Ala Ala Asp Met Ala Ala Ser Ala Asp Glu Glu Ala 1 5 10 15 Cys Met Tyr Ala Leu Gln Leu Val Ser Ser Ser Ile Leu Pro Met Thr 20 25 30 Leu Lys Asn Ala Ile Glu Leu Gly Leu Leu Glu Thr Leu Val Ala Ala 35 40 45 Gly Gly Lys Leu Leu Thr Pro Ala Glu Val Ala Ala Lys Leu Pro Ser 50 55 60 Thr Ala Asn Pro Ala Ala Ala Asp Met Val Asp Arg Met Leu Arg Leu 65 70 75 80 Leu Ala Ser Tyr Asn Val Val Ser Cys Thr Met Glu Glu Gly Lys Asp 85 90 95 Gly Arg Leu Ser Arg Arg Tyr Gly Ala Ala Pro Val Cys Lys Phe Leu 100 105 110 Thr Pro Asn Glu Asp Gly Val Ser Met Ala Ala Leu Ala Leu Met Asn 115 120 125 Gln Asp Lys Val Leu Met Glu Ser Trp Tyr Tyr Leu Lys Asp Ala Val 130 135 140 Leu Asp Gly Gly Ile Pro Phe Asn Lys Ala Tyr Gly Met Ser Ala Phe 145 150 155 160 Glu Tyr His Gly Thr Asp Pro Arg Phe Asn Arg Val Phe Asn Glu Gly 165 170 175 Met Lys Asn His Ser Ile Ile Ile Thr Lys Lys Leu Leu Glu Val Tyr 180 185 190 Lys Gly Phe Glu Gly Leu Gly Thr Ile Val Asp Val Gly Gly Gly Val 195 200 205 Gly Ala Ile Val Ala Ala Tyr Pro Ala Ile Lys Gly Ile Asn Phe Asp 210 215 220 Leu Pro His Val Ile Ser Glu Ala Pro Pro Phe Pro Gly Val Thr His 225 230 235 240 Val Gly Gly Asp Met Phe Gln Lys Val Pro Ser Gly Asp Ala Ile Leu 245 250 255 Met Lys Trp Ile Leu His Asp Trp Ser Asp Glu His Cys Ala Thr Leu 260 265 270 Leu Lys Asn Cys Tyr Asp Ala Leu Pro Ala His Gly Lys Val Val Leu 275 280 285 Val Glu Cys Ile Leu Pro Val Asn Pro Glu Ala Thr Pro Lys Ala Gln 290 295 300 Gly Val Phe His Val Asp Met Ile Met Leu Ala His Asn Pro Gly Gly 305 310 315 320 Arg Glu Arg Tyr Glu Arg Glu Phe Glu Ala Leu Ala Lys Gly Ala Gly 325 330 335 Phe Lys Ala Ile Lys Thr Thr Tyr Ile Tyr Ala Asn Ala Phe Ala Ile 340 345 350 Glu Phe Thr Lys 355 7 760 DNA Zea mays unsure (53) n = A, C, G or T 7 cgggggtatc cgagcccctc atgggtgccc tcctcgacgg ctacggcgcc gcnggcgggt 60 ttcgcggcgt cgccacgctc gtagacgtcg ggggaagctc cggcgcctgc ctcgagatga 120 tcatgcgcag ggtccccaca atcaccgagg gcatcaactt cgacctcccc gacgtcgtcg 180 ccgcagcgcc gcccatcgcc ggagtgaggc atgttggcgg agatatgttc aagtccatcc 240 cctccggtga tgccattttc atgaagtggg ttctgacgac gtggaccgac gacgagtgca 300 cggccatcct gaggaactgc cacgccgctc tgccggacgg cggcaagctc gtggcctgcn 360 agccggtggt gccggaggag acggacagca gcaccaggac gagggcgctg ctggagaacg 420 acatcttcgt catgaccacc taccggacgc agggagggat gcgctccgag gaggagttcc 480 gccacctcgg cgtcgacgcc gcaggcttca ccgccttccg agccatctat ctcgacccct 540 tctatgccgt cctcgagtat accaagtgat ctccactcca tccgcccaaa tctccttgcg 600 agttgaatag cagaataacg aacagataaa taaagctatt ccattcacgt tggaatccga 660 atctctgcct actgtctgta ctcaacgtta gcttctgtaa ccaggatctc tctttcaagc 720 atttccaagc ttttgatgac aaaatcataa tttcgagctc 760 8 188 PRT Zea mays UNSURE (120) Xaa = ANY AMINO ACID 8 Gly Val Ser Glu Pro Leu Met Gly Ala Leu Leu Asp Gly Tyr Gly Ala 1 5 10 15 Ala Gly Gly Phe Arg Gly Val Ala Thr Leu Val Asp Val Gly Gly Ser 20 25 30 Ser Gly Ala Cys Leu Glu Met Ile Met Arg Arg Val Pro Thr Ile Thr 35 40 45 Glu Gly Ile Asn Phe Asp Leu Pro Asp Val Val Ala Ala Ala Pro Pro 50 55 60 Ile Ala Gly Val Arg His Val Gly Gly Asp Met Phe Lys Ser Ile Pro 65 70 75 80 Ser Gly Asp Ala Ile Phe Met Lys Trp Val Leu Thr Thr Trp Thr Asp 85 90 95 Asp Glu Cys Thr Ala Ile Leu Arg Asn Cys His Ala Ala Leu Pro Asp 100 105 110 Gly Gly Lys Leu Val Ala Cys Xaa Pro Val Val Pro Glu Glu Thr Asp 115 120 125 Ser Ser Thr Arg Thr Arg Ala Leu Leu Glu Asn Asp Ile Phe Val Met 130 135 140 Thr Thr Tyr Arg Thr Gln Gly Gly Met Arg Ser Glu Glu Glu Phe Arg 145 150 155 160 His Leu Gly Val Asp Ala Ala Gly Phe Thr Ala Phe Arg Ala Ile Tyr 165 170 175 Leu Asp Pro Phe Tyr Ala Val Leu Glu Tyr Thr Lys 180 185 9 1342 DNA Oryza sativa 9 tagccatact gaccagagag gctcacatgg atccgtacac tagcagggct ccggcgagtg 60 gtggtgtcgc cgccggcgac gacgacgagg aggcggcgtg cctgcaggcg tttgagctaa 120 tgtgcatctt caccgtcccc atgacactga aggcggcgat cgagctcggc ctcctcgacg 180 cactagccgc cgccggcgac ggccgcgcac tgaccgcgga cgagctggcc gccgcgcggc 240 tcccggacgc ggcgccggac aaggccgagg cggcgtcctc ggtggaccgg atgctgcggc 300 tcctcgcgtc gttcgacgtc gtcaagtgct cgacggaggc cgggcccggc ggcgaacctc 360 cccggagacg atactcgccg gcgcccgtct gcaggttgtt caccgccggc ggcaacagcc 420 accgtggatc tctggccccc tcggtcttgt tcggcgtcga cgaggactac ctgtgcacct 480 ggcgtcagtt ggcggcggcg gtgggcggcg gcgggccgtc ggcgttcgag agggcgcacg 540 ggatgcggat gttcgagtac atggggacga accgccggct gaacacgctg ttcaaccagg 600 ccatggcgca gcagtccatg attgtgattg acaagctgct cgaccgcttc catgggttcg 660 acggcgtcgg cgtcctcgtc gacgtcggcg ggggcaccgg cgccaccctg gagatgatca 720 cctcccggta caagcatatc accggcgtta acttcgacct accccatgtc atctctcagg 780 ctccatctat tccgggtgtg aaacatatag ctggaaatat gtttgagagc atatctaata 840 ttggagatgc aattttctta aagatgatcc tccacatgca aaacgatgag gactgcatca 900 agatcctcaa gaattgccac caagccctgc cggacaatgg caaggtgatt gctgttgaga 960 ttgtcctccc gacgatccca gatctggccc aaacagcacg atacccgttc cagatggaca 1020 tgatcatgct cagcaattcc cggggaggaa aggagaggac agagctggag ttcgccaagc 1080 tagccacgga ctctggtttc agtggtgcct tgcgaacaac ctacatcttg gccaactatt 1140 gggttcttga gttcagcaag tagctctgaa aaatcatgtc aagttcaatt tgctaagcat 1200 tttaatgtgt gcatggttat ttcaatacca tacaaatggt gatcagaatc gctatatata 1260 ctgaacaata tatgtcaaat atacaatata aaatgtaaag tgtcccttaa aattgaaaaa 1320 aaaaaaaaaa aaaaaaaaaa aa 1342 10 378 PRT Oryza sativa 10 Met Asp Pro Tyr Thr Ser Arg Ala Pro Ala Ser Gly Gly Val Ala Ala 1 5 10 15 Gly Asp Asp Asp Glu Glu Ala Ala Cys Leu Gln Ala Phe Glu Leu Met 20 25 30 Cys Ile Phe Thr Val Pro Met Thr Leu Lys Ala Ala Ile Glu Leu Gly 35 40 45 Leu Leu Asp Ala Leu Ala Ala Ala Gly Asp Gly Arg Ala Leu Thr Ala 50 55 60 Asp Glu Leu Ala Ala Ala Arg Leu Pro Asp Ala Ala Pro Asp Lys Ala 65 70 75 80 Glu Ala Ala Ser Ser Val Asp Arg Met Leu Arg Leu Leu Ala Ser Phe 85 90 95 Asp Val Val Lys Cys Ser Thr Glu Ala Gly Pro Gly Gly Glu Pro Pro 100 105 110 Arg Arg Arg Tyr Ser Pro Ala Pro Val Cys Arg Leu Phe Thr Ala Gly 115 120 125 Gly Asn Ser His Arg Gly Ser Leu Ala Pro Ser Val Leu Phe Gly Val 130 135 140 Asp Glu Asp Tyr Leu Cys Thr Trp Arg Gln Leu Ala Ala Ala Val Gly 145 150 155 160 Gly Gly Gly Pro Ser Ala Phe Glu Arg Ala His Gly Met Arg Met Phe 165 170 175 Glu Tyr Met Gly Thr Asn Arg Arg Leu Asn Thr Leu Phe Asn Gln Ala 180 185 190 Met Ala Gln Gln Ser Met Ile Val Ile Asp Lys Leu Leu Asp Arg Phe 195 200 205 His Gly Phe Asp Gly Val Gly Val Leu Val Asp Val Gly Gly Gly Thr 210 215 220 Gly Ala Thr Leu Glu Met Ile Thr Ser Arg Tyr Lys His Ile Thr Gly 225 230 235 240 Val Asn Phe Asp Leu Pro His Val Ile Ser Gln Ala Pro Ser Ile Pro 245 250 255 Gly Val Lys His Ile Ala Gly Asn Met Phe Glu Ser Ile Ser Asn Ile 260 265 270 Gly Asp Ala Ile Phe Leu Lys Met Ile Leu His Met Gln Asn Asp Glu 275 280 285 Asp Cys Ile Lys Ile Leu Lys Asn Cys His Gln Ala Leu Pro Asp Asn 290 295 300 Gly Lys Val Ile Ala Val Glu Ile Val Leu Pro Thr Ile Pro Asp Leu 305 310 315 320 Ala Gln Thr Ala Arg Tyr Pro Phe Gln Met Asp Met Ile Met Leu Ser 325 330 335 Asn Ser Arg Gly Gly Lys Glu Arg Thr Glu Leu Glu Phe Ala Lys Leu 340 345 350 Ala Thr Asp Ser Gly Phe Ser Gly Ala Leu Arg Thr Thr Tyr Ile Leu 355 360 365 Ala Asn Tyr Trp Val Leu Glu Phe Ser Lys 370 375 11 1195 DNA Glycine max 11 gcacgagcat atcagtgata caaaagacaa gtaagaataa tcaagcaaga agaaatggaa 60 gaagaaaaaa gcttcaccta tgcaatgcag ctggtgaact ctagcgtgct atccatggcc 120 atgcactcag ccatagagct tggcattttt gacatcatag ccaaagcagg tgaaggtgcc 180 aaattatctg ccaaggacat tgcagccaag cttccatgca agaattcaga aggagccaca 240 atgttggatc gtatcctaag gctcctagta tgtcactcca tcattgactg cacagtggtt 300 gctgatcaac aacatggtcc tcctccacat ctgcaacggt tctatgccat gaaccctgtg 360 gccaaatact ttgcttccat tgatggtgct ggctcactag gccctttgat ggtcttgact 420 caggacaagg ccctccttca tagttggtac caattgaaag atgcaattct agaaggaggt 480 attcctttca acagggttca tggaaaacac gtgtttgaat attccgacat gaactcgagc 540 ttcaatcagc ttttcatggc agctatgaca aaccgtgcaa ctttaataat gaagaagatt 600 gttgaatcct acaaggggtt tgagcacctc aatagcctgg tggacgttgg aggtggcctt 660 ggtgtcacac ttaacatagt cacttctaaa taccctcaca ttaagggtat caattttgac 720 ttgccacatg tcatagaaca tgcctctacc tatcctggtg ttgagcatgt gggaggagat 780 atgtttgaaa gtgtgccaca aggagatgcc attttgatga tgtgtgtact tcatgattgg 840 agtgatgaat ggtgcttgaa ggtattaaag aattgttatg cttctattcc tagtgatgga 900 aaggtgattg ttgtggatgg aattcttcca tttgaaccaa agacaacagg tgcatcaaag 960 agcatttccc aatttgatgt actgatgatg actacaaacc caggagggaa ggagcgaagt 1020 gaagaggaat tcatggcatt ggcaaaagga gctggataca gtggcattag attcacatgc 1080 tttgtctctg acttatgggt tatggagttc ttcaagtaaa tgttgtatgt cacacatgct 1140 gctgcagatg gaataaaatg aaattagaaa ttgcaataaa aaaaaaaaaa aaaaa 1195 12 354 PRT Glycine max 12 Met Glu Glu Glu Lys Ser Phe Thr Tyr Ala Met Gln Leu Val Asn Ser 1 5 10 15 Ser Val Leu Ser Met Ala Met His Ser Ala Ile Glu Leu Gly Ile Phe 20 25 30 Asp Ile Ile Ala Lys Ala Gly Glu Gly Ala Lys Leu Ser Ala Lys Asp 35 40 45 Ile Ala Ala Lys Leu Pro Cys Lys Asn Ser Glu Gly Ala Thr Met Leu 50 55 60 Asp Arg Ile Leu Arg Leu Leu Val Cys His Ser Ile Ile Asp Cys Thr 65 70 75 80 Val Val Ala Asp Gln Gln His Gly Pro Pro Pro His Leu Gln Arg Phe 85 90 95 Tyr Ala Met Asn Pro Val Ala Lys Tyr Phe Ala Ser Ile Asp Gly Ala 100 105 110 Gly Ser Leu Gly Pro Leu Met Val Leu Thr Gln Asp Lys Ala Leu Leu 115 120 125 His Ser Trp Tyr Gln Leu Lys Asp Ala Ile Leu Glu Gly Gly Ile Pro 130 135 140 Phe Asn Arg Val His Gly Lys His Val Phe Glu Tyr Ser Asp Met Asn 145 150 155 160 Ser Ser Phe Asn Gln Leu Phe Met Ala Ala Met Thr Asn Arg Ala Thr 165 170 175 Leu Ile Met Lys Lys Ile Val Glu Ser Tyr Lys Gly Phe Glu His Leu 180 185 190 Asn Ser Leu Val Asp Val Gly Gly Gly Leu Gly Val Thr Leu Asn Ile 195 200 205 Val Thr Ser Lys Tyr Pro His Ile Lys Gly Ile Asn Phe Asp Leu Pro 210 215 220 His Val Ile Glu His Ala Ser Thr Tyr Pro Gly Val Glu His Val Gly 225 230 235 240 Gly Asp Met Phe Glu Ser Val Pro Gln Gly Asp Ala Ile Leu Met Met 245 250 255 Cys Val Leu His Asp Trp Ser Asp Glu Trp Cys Leu Lys Val Leu Lys 260 265 270 Asn Cys Tyr Ala Ser Ile Pro Ser Asp Gly Lys Val Ile Val Val Asp 275 280 285 Gly Ile Leu Pro Phe Glu Pro Lys Thr Thr Gly Ala Ser Lys Ser Ile 290 295 300 Ser Gln Phe Asp Val Leu Met Met Thr Thr Asn Pro Gly Gly Lys Glu 305 310 315 320 Arg Ser Glu Glu Glu Phe Met Ala Leu Ala Lys Gly Ala Gly Tyr Ser 325 330 335 Gly Ile Arg Phe Thr Cys Phe Val Ser Asp Leu Trp Val Met Glu Phe 340 345 350 Phe Lys 13 1308 DNA Triticum aestivum 13 ctcgtgccga attcggcacg agacaactat cagcagcacc agctcggcta tctccaaagt 60 ccgaacaagc agttaatata attatctgct aaatgggctc cactgccgtg gagaaggtcg 120 ctgtcgccac tggcgacgag gaggcgtgca tgtacgcggt gaagcttgca gcggcatcta 180 tccttccaat gaccctcaag aacgccatcg agctgggcat gctcgagatc ctcgtgggtg 240 ccggcgggaa gatgttgtca ccttcagagg tggcagcgca gcttccgtcg aaggccaacc 300 cggaggcacc ggttatggtg gaccgcatgc tgcggctgct ggcatcgaac aacgtcgtgt 360 catgcgaggt ggaggaaggt aaggacggcc tcctcgcccg tcgatacggc cccgcgcccg 420 tgtgtaagtg gctcacaccc aacgaggacg gcgcatccat ggctgggctg ctcctcatga 480 cccacgacaa ggtcactatg gagagctggt attatttgaa ggacgtggcc cttgaaggcg 540 gccaaccatt ccacagggcg cacgggatga cggcgtacga gtacaacagc acagacccac 600 gcgctaactg cttgttcaac gaggccatgc ttaaccactc caccatcatc accaagaagc 660 tcctcgagtt ctacaggggc ttcgacaacg tcgagaccct cgtggatgtc gccggtggcg 720 ttggtgccac agcccacgcc atcacctcaa agtacccgca catcaagggg gtaaacttcg 780 atctcccgca tgtcatatcc gaggcgccgc cctaccctgg cgtgcagcac atcgccggtg 840 acatgttcaa gaaggtgccc tccggcgatg ctatcctcct gaagtggatc ctccacaact 900 ggaccgacga ttactgtatg actcttctga ggaactgcta cgatgcgttg cccatgaatg 960 gcaaggtggt catcgtggag ggcatcctgc cggtgaaacc agatgcaatg cccagcacgc 1020 agacgatgtt ccaggtcgac atgatgatgc tgctgcacac cgcaggcggc aaggagaggg 1080 aactgagcga atttgaagag ctagcgaagg gcgctgggtt cagcacagtc aagaccagct 1140 acatctacag caccgcatgg gtcattgagt tcgtcaaata gatcactcta atattttctt 1200 gcttctgctc ctagtatcgg aatatgtact tttgagcttc cttttcctgc tgtccttagc 1260 atctcatgta atgtatcacc tcgtgccgaa ttcggcacga gctggtgc 1308 14 362 PRT Triticum aestivum 14 Met Gly Ser Thr Ala Val Glu Lys Val Ala Val Ala Thr Gly Asp Glu 1 5 10 15 Glu Ala Cys Met Tyr Ala Val Lys Leu Ala Ala Ala Ser Ile Leu Pro 20 25 30 Met Thr Leu Lys Asn Ala Ile Glu Leu Gly Met Leu Glu Ile Leu Val 35 40 45 Gly Ala Gly Gly Lys Met Leu Ser Pro Ser Glu Val Ala Ala Gln Leu 50 55 60 Pro Ser Lys Ala Asn Pro Glu Ala Pro Val Met Val Asp Arg Met Leu 65 70 75 80 Arg Leu Leu Ala Ser Asn Asn Val Val Ser Cys Glu Val Glu Glu Gly 85 90 95 Lys Asp Gly Leu Leu Ala Arg Arg Tyr Gly Pro Ala Pro Val Cys Lys 100 105 110 Trp Leu Thr Pro Asn Glu Asp Gly Ala Ser Met Ala Gly Leu Leu Leu 115 120 125 Met Thr His Asp Lys Val Thr Met Glu Ser Trp Tyr Tyr Leu Lys Asp 130 135 140 Val Ala Leu Glu Gly Gly Gln Pro Phe His Arg Ala His Gly Met Thr 145 150 155 160 Ala Tyr Glu Tyr Asn Ser Thr Asp Pro Arg Ala Asn Cys Leu Phe Asn 165 170 175 Glu Ala Met Leu Asn His Ser Thr Ile Ile Thr Lys Lys Leu Leu Glu 180 185 190 Phe Tyr Arg Gly Phe Asp Asn Val Glu Thr Leu Val Asp Val Ala Gly 195 200 205 Gly Val Gly Ala Thr Ala His Ala Ile Thr Ser Lys Tyr Pro His Ile 210 215 220 Lys Gly Val Asn Phe Asp Leu Pro His Val Ile Ser Glu Ala Pro Pro 225 230 235 240 Tyr Pro Gly Val Gln His Ile Ala Gly Asp Met Phe Lys Lys Val Pro 245 250 255 Ser Gly Asp Ala Ile Leu Leu Lys Trp Ile Leu His Asn Trp Thr Asp 260 265 270 Asp Tyr Cys Met Thr Leu Leu Arg Asn Cys Tyr Asp Ala Leu Pro Met 275 280 285 Asn Gly Lys Val Val Ile Val Glu Gly Ile Leu Pro Val Lys Pro Asp 290 295 300 Ala Met Pro Ser Thr Gln Thr Met Phe Gln Val Asp Met Met Met Leu 305 310 315 320 Leu His Thr Ala Gly Gly Lys Glu Arg Glu Leu Ser Glu Phe Glu Glu 325 330 335 Leu Ala Lys Gly Ala Gly Phe Ser Thr Val Lys Thr Ser Tyr Ile Tyr 340 345 350 Ser Thr Ala Trp Val Ile Glu Phe Val Lys 355 360 15 1458 DNA Oryza sativa 15 gcacgaggtt taaacgtgcc atgtagtgca ccaacacgcc atatactagt ttcagaattg 60 agacacactg atcattgtga gagagaagta gaccaaacaa ggcaagctcg catggcttcg 120 ggcattagca ggactccggc cacgggtgtc accgccggcg gcggcgacga cgaggaggcg 180 gcatggttgc acgcgcttga gctgatctcg ggcttcaccg tctccatgac actgaaggcg 240 gcgatccagc tcggactcat cgacgcactt accgccgccg ccgacggccg cgcgctgacc 300 gccggcgagc tggttgcgca gctcccggcg gtggacgatg ccgaggcggc gacctcggtg 360 gaccggatgc tgcggctcct ggcgtcgttc aacgtcgtca ggtgctcgac ggaggcgggg 420 cctggcggtg atcctctccg gcgctactcg ccggcgcctg tgtgcaggtg gttcaccgcc 480 ggcgacaacc accaagggtc tctggcaccc aggctcatgc tcgacgtcga cgaagacaat 540 ctgagcacct ggcatcagat ggcggcggcg gtcgtcagcg gtgggccatc ggcgttcgag 600 agggcgcacg ggatgccatt gtttgagtac atggggacga accaccggtt caatatgctg 660 ttcaaccagg ccatgtcgca gcagtccatg atggtgatga acaagctgct agaccgcttc 720 catgggtttg atggcatcag tgtcctcgtc gacgtcggcg ggggcaccgg cgtcaccctg 780 aagatgatca tctcccggta taagcacatt actggtgtca acttcgactt accccacgtc 840 atatctcagg ctccatctct tccgggtgtg aatcatgtag ctggaaatat gtttgagagc 900 gtacctaaag gagatgcaat tttcttgaag tcgatgctcc tacgaaacga tgaggagtgc 960 atcaagattc tcaagaactg ccactatgct ctctcagaca atgggaaggt gattgttgtt 1020 gatattgttc tccctgaaac cccaaaaccg gtacccgaag cacaaaaccc actccggatg 1080 gacgttatga tgctcaacaa tcttcgtgga ggaaagataa ggacagagca ggagtacgcg 1140 aagctagcta tggattctgg cttcagtggt tccttccgga caacctacat tttcgccaac 1200 tttatggcaa ttgaactatg caagtagctc ttgaaaatca tgtcaagttc gtattactcc 1260 cttcatcact aactgaactt ttggctatgt atgtagacaa tcattttgct cagatatctt 1320 gtccatatgt acagccaaat gctcacgaag gagtatgtat ttcaatgtgt aattgtgtat 1380 ggctaacact ataccattca atggtctgaa aattaaaaac ttttcttcaa taataaaaaa 1440 aaaaaaaaaa aaaaaaaa 1458 16 371 PRT Oryza sativa 16 Met Ala Ser Gly Ile Ser Arg Thr Pro Ala Thr Gly Val Thr Ala Gly 1 5 10 15 Gly Gly Asp Asp Glu Glu Ala Ala Trp Leu His Ala Leu Glu Leu Ile 20 25 30 Ser Gly Phe Thr Val Ser Met Thr Leu Lys Ala Ala Ile Gln Leu Gly 35 40 45 Leu Ile Asp Ala Leu Thr Ala Ala Ala Asp Gly Arg Ala Leu Thr Ala 50 55 60 Gly Glu Leu Val Ala Gln Leu Pro Ala Val Asp Asp Ala Glu Ala Ala 65 70 75 80 Thr Ser Val Asp Arg Met Leu Arg Leu Leu Ala Ser Phe Asn Val Val 85 90 95 Arg Cys Ser Thr Glu Ala Gly Pro Gly Gly Asp Pro Leu Arg Arg Tyr 100 105 110 Ser Pro Ala Pro Val Cys Arg Trp Phe Thr Ala Gly Asp Asn His Gln 115 120 125 Gly Ser Leu Ala Pro Arg Leu Met Leu Asp Val Asp Glu Asp Asn Leu 130 135 140 Ser Thr Trp His Gln Met Ala Ala Ala Val Val Ser Gly Gly Pro Ser 145 150 155 160 Ala Phe Glu Arg Ala His Gly Met Pro Leu Phe Glu Tyr Met Gly Thr 165 170 175 Asn His Arg Phe Asn Met Leu Phe Asn Gln Ala Met Ser Gln Gln Ser 180 185 190 Met Met Val Met Asn Lys Leu Leu Asp Arg Phe His Gly Phe Asp Gly 195 200 205 Ile Ser Val Leu Val Asp Val Gly Gly Gly Thr Gly Val Thr Leu Lys 210 215 220 Met Ile Ile Ser Arg Tyr Lys His Ile Thr Gly Val Asn Phe Asp Leu 225 230 235 240 Pro His Val Ile Ser Gln Ala Pro Ser Leu Pro Gly Val Asn His Val 245 250 255 Ala Gly Asn Met Phe Glu Ser Val Pro Lys Gly Asp Ala Ile Phe Leu 260 265 270 Lys Ser Met Leu Leu Arg Asn Asp Glu Glu Cys Ile Lys Ile Leu Lys 275 280 285 Asn Cys His Tyr Ala Leu Ser Asp Asn Gly Lys Val Ile Val Val Asp 290 295 300 Ile Val Leu Pro Glu Thr Pro Lys Pro Val Pro Glu Ala Gln Asn Pro 305 310 315 320 Leu Arg Met Asp Val Met Met Leu Asn Asn Leu Arg Gly Gly Lys Ile 325 330 335 Arg Thr Glu Gln Glu Tyr Ala Lys Leu Ala Met Asp Ser Gly Phe Ser 340 345 350 Gly Ser Phe Arg Thr Thr Tyr Ile Phe Ala Asn Phe Met Ala Ile Glu 355 360 365 Leu Cys Lys 370 17 1314 DNA Glycine max unsure (472) n = A, C, G or T 17 cacaagctca cagagcaaga acactgttcc aatacggaat ctaaggcaaa gcaaaccaaa 60 catcttgaat catgggttca acaggtgaga ctcagattac tccaacccat gtatctgatg 120 aagaggcaaa ccttttcgcc atgcaactag ccagtgcctc agtactccct atggttctca 180 aatcagctct tgagcttgat ctgttggaaa tcatagccaa ggctggccct ggtgttcacc 240 tttccccctc cgacattgct tctcggctcc caacacacaa ccctgatgca cccgttatgt 300 tggaccgtat attgcgcctc ttggcttgct acaatatcct ctctttttct cttcgcactc 360 tccctcatgg caaggttgag aggctctatg gtctcgcccc tgttgctaag tacttggtca 420 ggaacgaaga tggtgtctcc attgctgctc tcaacctcat gaaccaggac anaatcctca 480 tggaaagctg gtactatttg aaagatgcag tccttgaagg gggtattcca tttaacaaag 540 catatggaat gacagccttt gaataccatg gaacggatcc aaggtttaac aaggttttca 600 acaaggggat ggctgatcac tctaccatta caatgaagaa aattcttgag acctacacag 660 gctttgaggg acttaaatcc ctggttgatg ttggtggagg aactggagct gtagtcaaca 720 tgattgtctc aaagtatccc actattaagg gcattaattt tgatttgccc catgtcattg 780 aagatgcccc atcttatcca ggagtggaac atgttggtgg agatatgttt gtcagtgttc 840 caaaagctga tgctattttt atgaagtgga tttgccacga ttggagtgat gagcactgct 900 tgaagttttt gaagaactgc tatgaggcac taccagataa tgggaaagtg attgtggcgg 960 aatgcattct tccggtggct ccagactcta gcttggccac aaagggtgtg gttcacatcg 1020 atgtgatcat gttggctcac aatccaggtg gggaaagaga gaacaagaga aagagtttga 1080 ggctctgggc caaaggctct ggattccaag gtttccaagt ccctgtgctg tgctttcaat 1140 acctaccgtc aatggnaatt tctcaaaaaa gggtttaagn tcttttggcg tggattcata 1200 atcaaagttg caatttggga ttttgacttt tgagactccg gcttgggggt gctaacctta 1260 cnaaatggtt ttccccggga aaaacttaaa tttcttccaa angccttatg aaaa 1314 18 358 PRT Glycine max UNSURE (134) Xaa = ANY AMINO ACID 18 Met Gly Ser Thr Gly Glu Thr Gln Ile Thr Pro Thr His Val Ser Asp 1 5 10 15 Glu Glu Ala Asn Leu Phe Ala Met Gln Leu Ala Ser Ala Ser Val Leu 20 25 30 Pro Met Val Leu Lys Ser Ala Leu Glu Leu Asp Leu Leu Glu Ile Ile 35 40 45 Ala Lys Ala Gly Pro Gly Val His Leu Ser Pro Ser Asp Ile Ala Ser 50 55 60 Arg Leu Pro Thr His Asn Pro Asp Ala Pro Val Met Leu Asp Arg Ile 65 70 75 80 Leu Arg Leu Leu Ala Cys Tyr Asn Ile Leu Ser Phe Ser Leu Arg Thr 85 90 95 Leu Pro His Gly Lys Val Glu Arg Leu Tyr Gly Leu Ala Pro Val Ala 100 105 110 Lys Tyr Leu Val Arg Asn Glu Asp Gly Val Ser Ile Ala Ala Leu Asn 115 120 125 Leu Met Asn Gln Asp Xaa Ile Leu Met Glu Ser Trp Tyr Tyr Leu Lys 130 135 140 Asp Ala Val Leu Glu Gly Gly Ile Pro Phe Asn Lys Ala Tyr Gly Met 145 150 155 160 Thr Ala Phe Glu Tyr His Gly Thr Asp Pro Arg Phe Asn Lys Val Phe 165 170 175 Asn Lys Gly Met Ala Asp His Ser Thr Ile Thr Met Lys Lys Ile Leu 180 185 190 Glu Thr Tyr Thr Gly Phe Glu Gly Leu Lys Ser Leu Val Asp Val Gly 195 200 205 Gly Gly Thr Gly Ala Val Val Asn Met Ile Val Ser Lys Tyr Pro Thr 210 215 220 Ile Lys Gly Ile Asn Phe Asp Leu Pro His Val Ile Glu Asp Ala Pro 225 230 235 240 Ser Tyr Pro Gly Val Glu His Val Gly Gly Asp Met Phe Val Ser Val 245 250 255 Pro Lys Ala Asp Ala Ile Phe Met Lys Trp Ile Cys His Asp Trp Ser 260 265 270 Asp Glu His Cys Leu Lys Phe Leu Lys Asn Cys Tyr Glu Ala Leu Pro 275 280 285 Asp Asn Gly Lys Val Ile Val Ala Glu Cys Ile Leu Pro Val Ala Pro 290 295 300 Asp Ser Ser Leu Ala Thr Lys Gly Val Val His Ile Asp Val Ile Met 305 310 315 320 Leu Ala His Asn Pro Gly Gly Glu Arg Glu Asn Lys Arg Lys Ser Leu 325 330 335 Arg Leu Trp Ala Lys Gly Ser Gly Phe Gln Gly Phe Gln Val Leu Cys 340 345 350 Cys Ala Phe Asn Thr Tyr 355 19 926 DNA Triticum aestivum unsure (627)..(628) n = A, C, G or T 19 aacatgggct ccaccgcagc cgacatggcc gcctccgccg acgaggaggc gtgcatgtat 60 gctctccagc tcgtctcgtc gtcgatcctc ccgatgacgc tcaagaacgc catcgagctg 120 ggtctcctgg agaccctggt ggccgccggc ggcaagctgc tgacgcccgc cgaggtggca 180 gccaagctcc cgtccacggc gaatcccgcc gcggcggaca tggtggaccg catgctccgg 240 ctgctggcct cgtacaacgt ggtgtcgtgc acgatggagg agggcaagga cggccggctg 300 tcccggcggt acggcgccgc gcccgtgtgc aagttcctca cccccaacga agacggcgtc 360 tccatggcgg cgctcgcgct catgaaccag gacaaggtcc tcatggagag ctggtactac 420 ctgaaggacg cggtccttga cggcggcatc ccgttcaaca aggcgtacgg gatgtcggcg 480 ttcgagtacc acggcacgga cccgcgcttc aaccgcgtct tcaacgaggg gatgaagaac 540 cactccatca tcatcaccaa gaagctcctc gaggtctaca agggcttcga gggcctcggc 600 accatcgtca gtttgggccg gcgcgtnngg cgccatcgtc gccgcctacc cggccatcaa 660 gggcatcaac ttcgacctcc cccacgtcat ctccgaaggc gccaccgttc ccgggcgtca 720 ccacgtcggc ggcgaatttc cagaaggtgc ctccgggcga cgccatcctc atgagtgggg 780 ttctccaacg actgggagcg acgaanaact gcgcgacgct gctcaaagaa tgtacnaagc 840 ctgccggnga aggaagntgg ggnccntgga ntgaactgcg ggtnaaccgg nggcaaccca 900 aggcnagggg attcaantca aattta 926 20 231 PRT Triticum aestivum UNSURE (208) Xaa = ANY AMINO ACID 20 Met Gly Ser Thr Ala Ala Asp Met Ala Ala Ser Ala Asp Glu Glu Ala 1 5 10 15 Cys Met Tyr Ala Leu Gln Leu Val Ser Ser Ser Ile Leu Pro Met Thr 20 25 30 Leu Lys Asn Ala Ile Glu Leu Gly Leu Leu Glu Thr Leu Val Ala Ala 35 40 45 Gly Gly Lys Leu Leu Thr Pro Ala Glu Val Ala Ala Lys Leu Pro Ser 50 55 60 Thr Ala Asn Pro Ala Ala Ala Asp Met Val Asp Arg Met Leu Arg Leu 65 70 75 80 Leu Ala Ser Tyr Asn Val Val Ser Cys Thr Met Glu Glu Gly Lys Asp 85 90 95 Gly Arg Leu Ser Arg Arg Tyr Gly Ala Ala Pro Val Cys Lys Phe Leu 100 105 110 Thr Pro Asn Glu Asp Gly Val Ser Met Ala Ala Leu Ala Leu Met Asn 115 120 125 Gln Asp Lys Val Leu Met Glu Ser Trp Tyr Tyr Leu Lys Asp Ala Val 130 135 140 Leu Asp Gly Gly Ile Pro Phe Asn Lys Ala Tyr Gly Met Ser Ala Phe 145 150 155 160 Glu Tyr His Gly Thr Asp Pro Arg Phe Asn Arg Val Phe Asn Glu Gly 165 170 175 Met Lys Asn His Ser Ile Ile Ile Thr Lys Lys Leu Leu Glu Val Tyr 180 185 190 Lys Gly Phe Glu Gly Leu Gly Thr Ile Val Ser Leu Ala Gly Ala Xaa 195 200 205 Gly Ala Ile Val Ala Ala Tyr Pro Ala Ile Lys Gly Ile Asn Phe Asp 210 215 220 Leu Pro His Val Ile Ser Glu 225 230 21 603 DNA Oryza sativa unsure (506) n = A, C, G or T 21 gccatactga ccagagaggc tcacatggat ccgtacacta gcagggctcc ggcgagtggt 60 ggtgtcgccg ccggcgacga cgacgaggag gcggcgtgcc tgcaggcgtt tgagctaatg 120 tgcatcttca ccgtccccat gacactgaag gcggcgatcg agctcggcct cctcgacgca 180 ctagccgccg ccggcgacgg ccgcgcactg accgcggacg agctggccgc cgcgcggctc 240 ccggacgcgg cgccggacaa ggccgaggcg gcgtcctcgg tggaccggat gctgcggctc 300 ctcgcgtcgt tcgacgtcgt caagtgctcg acggaggccg ggcccggcgg cgaacctccc 360 cgggagacga tactcgccgg cgcccgtctg caagttgttc accgccggcg gcaacagcca 420 ccgtggatct ctggccccct cggtcttgtt cggcgtcgac gaggactacc tgtgcactgg 480 cgtagttggc ggcggcggtg ggccgncngc nggccgtcgg cgttcgaana nggccaacgg 540 gatccggatg ttcnagtaca tgggaacaaa cgccggnnga aaccggtcaa caagcaatgg 600 cga 603 22 109 PRT Oryza sativa 22 Met Asp Pro Tyr Thr Ser Arg Ala Pro Ala Ser Gly Gly Val Ala Ala 1 5 10 15 Gly Asp Asp Asp Glu Glu Ala Ala Cys Leu Gln Ala Phe Glu Leu Met 20 25 30 Cys Ile Phe Thr Val Pro Met Thr Leu Lys Ala Ala Ile Glu Leu Gly 35 40 45 Leu Leu Asp Ala Leu Ala Ala Ala Gly Asp Gly Arg Ala Leu Thr Ala 50 55 60 Asp Glu Leu Ala Ala Ala Arg Leu Pro Asp Ala Ala Pro Asp Lys Ala 65 70 75 80 Glu Ala Ala Ser Ser Val Asp Arg Met Leu Arg Leu Leu Ala Ser Phe 85 90 95 Asp Val Val Lys Cys Ser Thr Glu Ala Gly Pro Gly Gly 100 105 23 511 DNA Glycine max unsure (264) n = A, C, G or T 23 catatcagtg atacaaaaga caagtaagaa taatcaagca agaagaaatg gaagaagaaa 60 aaagcttcac ctatgcaatg cagctggtga actctagcgt gctatccatg gccatgcact 120 cagccataga gcttggcatt tttgacatca tagccaaagc aggtgaaggt gccaaattat 180 ctgccaagga cattgcagcc aagcttccat gcaagaattc agaaggagcc acaatgttgg 240 atcgtatcct aaggctccta gtangtcact ccatcattga ctgcacagtg gttgctgatc 300 aacaacatgg tcctcctcca catctgcaac ggttctatgc catgaaccct gtggncaaat 360 actttgcttc cattgatggt gctggntcac taagcccttt gatggtcntt gactcaagac 420 aagggcctcc ttcanagttt ggtaccaatt gaaagatgca attctagaaa gaggnnttcc 480 cttcaacaag ggttcaaggg aaacacgtgt t 511 24 82 PRT Glycine max UNSURE (74) Xaa = ANY AMINO ACID 24 Glu Met Glu Glu Glu Lys Ser Phe Thr Tyr Ala Met Gln Leu Val Asn 1 5 10 15 Ser Ser Val Leu Ser Met Ala Met His Ser Ala Ile Glu Leu Gly Ile 20 25 30 Phe Asp Ile Ile Ala Lys Ala Gly Glu Gly Ala Lys Leu Ser Ala Lys 35 40 45 Asp Ile Ala Ala Lys Leu Pro Cys Lys Asn Ser Glu Gly Ala Thr Met 50 55 60 Leu Asp Arg Ile Leu Arg Leu Leu Val Xaa His Ser Ile Ile Asp Cys 65 70 75 80 Thr Val 25 849 DNA Triticum aestivum unsure (9) n = A, C, G or T 25 gaagcccgnc ngtttagtgc cncccagggg agccaccatg ttgntgtcct ataccnanna 60 ggtctttggg gantgtttta ttgaggaggt gccnttgagg ggccacccat tccacagggn 120 gacgggttac ggntagatac acacacaacc cangngttaa ttgnttgttn acggaggcca 180 tgttacantn ccccccatca tcaccaagaa gctcctcgat ttctacaggg gcttngacaa 240 cgtcgagacc ctngttgatg tcgccggtgg cgttgtncca cagcccacgc catcacntca 300 aagtacccgc acatcaaggg ggtaaacttc gatctcccgc atgtcatatc cgaggcgccg 360 cccttacctg gcgtgcagca catcgccggt gacatgttca agaagntgcc ctccggcgat 420 gctatcctcc tgaagtggat cctccacaac tggaccgacg attactgtat gactcttctg 480 aggaactgct acgatgcgtt gcccatgaat ggcaaggtgg tcatcgtgga gggcatcctg 540 ccggtgaaac cagatgcaat gcccagcacg cagacgatgt tccaggtcga catgatgatg 600 ctgctgcaca ccgcaggcgg caaggagagg gaactgagcg aatttgaaga gctagcgaag 660 ggcgctgggt tcagcagtca agaccagcta catctacagc accgcatggt cattgagttc 720 gtcaaataga tcactctaat attttcttgc ttctgctcct agtatcggaa tatgtacttt 780 tgagcttcct tttcctgctg tccttagcat ctcatgtaat gtatcacctc gtgccgaatt 840 cggcacgag 849 26 174 PRT Triticum aestivum UNSURE (13) Xaa = ANY AMINO ACID 26 Ile Ile Thr Lys Lys Leu Leu Asp Phe Tyr Arg Gly Xaa Asp Asn Val 1 5 10 15 Glu Thr Leu Val Asp Val Ala Gly Gly Val Xaa Xaa Thr Ala His Ala 20 25 30 Ile Thr Ser Lys Tyr Pro His Ile Lys Gly Val Asn Phe Asp Leu Pro 35 40 45 His Val Ile Ser Glu Ala Pro Pro Leu Pro Gly Val Gln His Ile Ala 50 55 60 Gly Asp Met Phe Lys Lys Xaa Pro Ser Gly Asp Ala Ile Leu Leu Lys 65 70 75 80 Trp Ile Leu His Asn Trp Thr Asp Asp Tyr Cys Met Thr Leu Leu Arg 85 90 95 Asn Cys Tyr Asp Ala Leu Pro Met Asn Gly Lys Val Val Ile Val Glu 100 105 110 Gly Ile Leu Pro Val Lys Pro Asp Ala Met Pro Ser Thr Gln Thr Met 115 120 125 Phe Gln Val Asp Met Met Met Leu Leu His Thr Ala Gly Gly Lys Glu 130 135 140 Arg Glu Leu Ser Glu Phe Glu Glu Leu Ala Lys Gly Ala Gly Phe Ser 145 150 155 160 Ala Val Lys Thr Ser Tyr Ile Tyr Ser Thr Ala Trp Ser Leu 165 170 27 627 DNA Oryza sativa unsure (404) n = A, C, G or T 27 gtttaaacgt gccatgtagt gcaccaacac gccatatact agtttcagaa ttgagacaca 60 ctgatcattg tgagagagaa gtagaccaaa caaggcaagc tcgcatggct tcgggcatta 120 gcaggactcc ggccacgggt gtcaccgccg gcggcggcga cgacgaggag gcggcatggt 180 tgcacgcgct tgagctgatc tcgggcttca ccgtctccat gacactgaag gcggcgatcc 240 agctcggact catcgacgca cttaccgccg ccgccgacgg ccgcgcgctg accgccggcg 300 agcgggttgc gcagctcccg gcggtggacg atgccgaggc ggcgacctcg gtggaccgga 360 tgctgcggct cctggcgtcg ttcaacgtcg tcaggtgctc gacngaggcg gggcctggcg 420 gtgatcctct ccggcgctac tcgccggcgc ctgtgtncaa gtggntcacc gccggggaca 480 accacaangg tctctggcan ccaagctcat gctcgacttc gacnaagaca tctgagcact 540 ggcatcaaat ggnggcgggg gtcgtancgg tgggcatcgg cttccaaaag gccacgtnat 600 gaanaantgc tanacgctcc atggttt 627 28 123 PRT Oryza sativa UNSURE (118) Xaa = ANY AMINO ACID 28 Met Ala Ser Gly Ile Ser Arg Thr Pro Ala Thr Gly Val Thr Ala Gly 1 5 10 15 Gly Gly Asp Asp Glu Glu Ala Ala Trp Leu His Ala Leu Glu Leu Ile 20 25 30 Ser Gly Phe Thr Val Ser Met Thr Leu Lys Ala Ala Ile Gln Leu Gly 35 40 45 Leu Ile Asp Ala Leu Thr Ala Ala Ala Asp Gly Arg Ala Leu Thr Ala 50 55 60 Gly Glu Arg Val Ala Gln Leu Pro Ala Val Asp Asp Ala Glu Ala Ala 65 70 75 80 Thr Ser Val Asp Arg Met Leu Arg Leu Leu Ala Ser Phe Asn Val Val 85 90 95 Arg Cys Ser Thr Glu Ala Gly Pro Gly Gly Asp Pro Leu Arg Arg Tyr 100 105 110 Ser Pro Ala Pro Val Xaa Lys Trp Xaa Thr Ala 115 120 

What is claimed is:
 1. An isolated polynucleotide comprising a first nucleotide sequence encoding a polypeptide of at least 305 amino acids that has at least 92% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14 and 16, or a second nucleotide sequence comprising the complement of the first nucleotide sequence.
 2. The isolated polynucleotide of claim 1, wherein the first nucleotide sequence consists of a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 1 1, 13 and 15 that codes for the polypeptide selected from the group consisting of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14 and
 16. 3. The isolated polynucleotide of claim 1 wherein the nucleotide sequences are DNA.
 4. The isolated polynucleotide of claim 1 wherein the nucleotide sequences are RNA.
 5. A chimeric gene comprising the isolated polynucleotide of claim 1 operably linked to suitable regulatory sequences.
 6. An isolated host cell comprising the chimeric gene of claim
 5. 7. A host cell comprising an isolated polynucleotide of claim
 1. 8. The host cell of claim 7 wherein the host cell is selected from the group consisting of yeast, bacteria, plant, and virus.
 9. A virus comprising the isolated polynucleotide of claim
 1. 10. A polypeptide of at least 305 amino acids that has at least 92% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14 and
 16. 11. A method of selecting an isolated polynucleotide that affects the level of expression of a phenylpropanoid metabolism polypeptide in a plant cell, the method comprising the steps of: (a) constructing an isolated polynucleotide comprising a nucleotide sequence of at least one of 30 contiguous nucleotides derived from an isolated polynucleotide of claim 1; (b) introducing the isolated polynucleotide into a plant cell; (c) measuring the level of a polypeptide in the plant cell containing the polynucleotide; and (d) comparing the level of polypeptide in the plant cell containing the isolated polynucleotide with the level of polypeptide in a plant cell that does not contain the isolated polynucleotide.
 12. The method of claim 11 wherein the isolated polynucleotide consists of a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13 and 15 that codes for the polypeptide selected from the group consisting of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14 and
 16. 13. A method of selecting an isolated polynucleotide that affects the level of expression of a phenylpropanoid metabolism polypeptide in a plant cell, the method comprising the steps of: (a) constructing an isolated polynucleotide of claim 1; (b) introducing the isolated polynucleotide into a plant cell; (c) measuring the level in vivo or in-vitro of polypeptide in the plant cell containing the polynucleotide; and (d) comparing the level of polypeptide in the plant cell containing the isolated polynucleotide with the level of polypeptide in a plant cell that does not contain the polynucleotide.
 14. A method of obtaining a nucleic acid fragment encoding a phenylpropanoid metabolism polypeptide comprising the steps of: (a) synthesizing an oligonucleotide primer comprising a nucleotide sequence of at least one of 30 contiguous nucleotides derived from a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13 and 15 and the complement of such nucleotide sequences; and (b) amplifying a nucleic acid sequence using the oligonucleotide primer.
 15. A method of obtaining a nucleic acid fragment encoding a phenylpropanoid metabolism polypeptide comprising the steps of: (a) probing a cDNA or genomic library with an isolated polynucleotide comprising at least one of 30 contiguous nucleotides derived from a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13 and 15 and the complement of such nucleotide sequences; (b) identifying a DNA clone that hybridizes with the isolated polynucleotide; (c) isolating the identified DNA clone; and (d) sequencing the cDNA or genomic fragment that comprises the isolated DNA clone.
 16. A composition comprising the isolated polynucleotide of claim
 1. 17. A composition comprising the isolated polynucleotide of claim
 10. 18. An isolated polynucleotide comprising the nucleotide sequence having at least one of 30 contiguous nucleotides derived from a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, and 13 and the complement of such sequences.
 19. An expression cassette comprising an isolated polynucleotide of claim 1 operably linked to a promoter.
 20. A method for positive selection of a transformed cell comprising: (a) transforming a host cell with the chimeric gene of claim 5 or an expression cassette of claim 20; and (b) growing the transformed host cell under conditions which allow expression of the polynucleotide in an amount sufficient to complement a null mutant and alter methylation of both caffeic acid and 5-hydroxyferulic acid to provide a positive selection means.
 22. The method of any of claims 21 or 23 wherein the plant cell is a monocot.
 23. The method of any of claims 21 or 23 wherein the plant cell is a dicot.
 24. An isolated polynucleotide comprising a first nucleotide sequence encoding a polypeptide of at least 50 amino acids that has at least 80% identity based on the Clustal method of alignment when compared to a polypeptide selected from the group consisting of SEQ ID NOs: 18, 20, 22, 24, 26 and 28 or a second nucleotide sequence comprising the complement of the first nucleotide sequence. 